diff --git a/src/db/db/dbAsIfFlatRegion.cc b/src/db/db/dbAsIfFlatRegion.cc
index 7129440a2..c2e9f2f08 100644
--- a/src/db/db/dbAsIfFlatRegion.cc
+++ b/src/db/db/dbAsIfFlatRegion.cc
@@ -1061,8 +1061,14 @@ AsIfFlatRegion::run_check (db::edge_relation_type rel, bool different_polygons,
     others.push_back (begin_merged ());
   } else {
     foreign.push_back (false);
-    others.push_back (other->begin ());
-    other_is_merged = other->is_merged ();
+    if (options.whole_edges) {
+      //  NOTE: whole edges needs both inputs merged
+      others.push_back (other->begin_merged ());
+      other_is_merged = true;
+    } else {
+      others.push_back (other->begin ());
+      other_is_merged = other->is_merged ();
+    }
     has_other = true;
   }
 
diff --git a/src/db/db/dbDeepRegion.cc b/src/db/db/dbDeepRegion.cc
index d4ba5d946..21284422c 100644
--- a/src/db/db/dbDeepRegion.cc
+++ b/src/db/db/dbDeepRegion.cc
@@ -1645,8 +1645,14 @@ DeepRegion::run_check (db::edge_relation_type rel, bool different_polygons, cons
     if (! other_deep) {
       return db::AsIfFlatRegion::run_check (rel, different_polygons, other, d, options);
     }
-    other_layer = other_deep->deep_layer ().layer ();
-    other_is_merged = other->is_merged ();
+    if (options.whole_edges) {
+      //  NOTE: whole edges needs both inputs merged
+      other_layer = other_deep->merged_deep_layer ().layer ();
+      other_is_merged = true;
+    } else {
+      other_layer = other_deep->deep_layer ().layer ();
+      other_is_merged = other->is_merged ();
+    }
   }
 
   const db::DeepLayer &polygons = merged_deep_layer ();
diff --git a/src/db/db/dbRegionUtils.h b/src/db/db/dbRegionUtils.h
index dbb1ccc4b..cd759cb4f 100644
--- a/src/db/db/dbRegionUtils.h
+++ b/src/db/db/dbRegionUtils.h
@@ -844,9 +844,13 @@ protected:
     if (layer == 0) {
       edge2edge_check<Output>::put (db::EdgePair (edge, edge.swapped_points ()), false);
     }
+#if 0
+    //  NOTE: second-input negative edge output isn't worth a lot as the second input often is not merged, hence
+    //  the outer edges to not represent the actual contour.
     if (layer == 1) {
       edge2edge_check<Output>::put (db::EdgePair (edge.swapped_points (), edge), false);
     }
+#endif
   }
 };
 
diff --git a/src/db/db/gsiDeclDbRegion.cc b/src/db/db/gsiDeclDbRegion.cc
index c8ee01b40..86a6dd4e5 100644
--- a/src/db/db/gsiDeclDbRegion.cc
+++ b/src/db/db/gsiDeclDbRegion.cc
@@ -2589,7 +2589,7 @@ Class<db::Region> decl_Region (decl_dbShapeCollection, "db", "Region",
     "@param max_projection The upper limit of the projected length of one edge onto another\n"
     "@param opposite_filter Specifies a filter mode for errors happening on opposite sides of inputs shapes\n"
     "@param rect_filter Specifies an error filter for rectangular input shapes\n"
-    "@param negative If true, edges not violation the condition will be output as pseudo-edge pairs\n"
+    "@param negative Negative output from the first input\n"
     "\n"
     "If \"whole_edges\" is true, the resulting \\EdgePairs collection will receive the whole "
     "edges which contribute in the width check.\n"
@@ -2617,9 +2617,15 @@ Class<db::Region> decl_Region (decl_dbShapeCollection, "db", "Region",
     "\"opposite_filter\" specifies whether to require or reject errors happening on opposite sides of a figure. "
     "\"rect_filter\" allows suppressing specific error configurations on rectangular input figures.\n"
     "\n"
+    "If \"negative\" is true, only edges from the first input are output as pseudo edge-pairs where the distance is "
+    "larger or equal to the limit. This is a way to flag the parts of the first input where the distance to the second "
+    "input is bigger. Note that only the first input's edges are output. The output is still edge pairs, but each edge pair "
+    "contains one edge from the original input and the reverse version of the edge as the second edge.\n"
+    "\n"
     "Merged semantics applies for the input of this method (see \\merged_semantics= for a description of this concept)\n"
     "\n"
-    "The 'shielded', 'negative', 'not_opposite' and 'rect_sides' options have been introduced in version 0.27."
+    "The 'shielded', 'negative', 'not_opposite' and 'rect_sides' options have been introduced in version 0.27. "
+    "The interpretation of the 'negative' flag has been restriced to first-layout only output in 0.27.1.\n"
   ) +
   method_ext ("overlap_check", &overlap2, gsi::arg ("other"), gsi::arg ("d"), gsi::arg ("whole_edges", false), gsi::arg ("metrics", db::metrics_type::Euclidian, "Euclidian"), gsi::arg ("ignore_angle", tl::Variant (), "default"), gsi::arg ("min_projection", tl::Variant (), "0"), gsi::arg ("max_projection", tl::Variant (), "max"), gsi::arg ("shielded", true), gsi::arg ("opposite_filter", db::NoOppositeFilter, "NoOppositeFilter"), gsi::arg ("rect_filter", db::NoSideAllowed, "NoSideAllowed"), gsi::arg ("negative", false),
     "@brief Performs an overlap check with options\n"
@@ -2632,7 +2638,7 @@ Class<db::Region> decl_Region (decl_dbShapeCollection, "db", "Region",
     "@param max_projection The upper limit of the projected length of one edge onto another\n"
     "@param opposite_filter Specifies a filter mode for errors happening on opposite sides of inputs shapes\n"
     "@param rect_filter Specifies an error filter for rectangular input shapes\n"
-    "@param negative If true, edges not violation the condition will be output as pseudo-edge pairs\n"
+    "@param negative Negative output from the first input\n"
     "\n"
     "If \"whole_edges\" is true, the resulting \\EdgePairs collection will receive the whole "
     "edges which contribute in the width check.\n"
@@ -2660,9 +2666,15 @@ Class<db::Region> decl_Region (decl_dbShapeCollection, "db", "Region",
     "\"opposite_filter\" specifies whether to require or reject errors happening on opposite sides of a figure. "
     "\"rect_filter\" allows suppressing specific error configurations on rectangular input figures.\n"
     "\n"
+    "If \"negative\" is true, only edges from the first input are output as pseudo edge-pairs where the overlap is "
+    "larger or equal to the limit. This is a way to flag the parts of the first input where the overlap vs. the second "
+    "input is bigger. Note that only the first input's edges are output. The output is still edge pairs, but each edge pair "
+    "contains one edge from the original input and the reverse version of the edge as the second edge.\n"
+    "\n"
     "Merged semantics applies for the input of this method (see \\merged_semantics= for a description of this concept)\n"
     "\n"
-    "The 'shielded', 'negative', 'not_opposite' and 'rect_sides' options have been introduced in version 0.27."
+    "The 'shielded', 'negative', 'not_opposite' and 'rect_sides' options have been introduced in version 0.27. "
+    "The interpretation of the 'negative' flag has been restriced to first-layout only output in 0.27.1.\n"
   ) +
   method_ext ("enclosing_check", &enclosing2, gsi::arg ("other"), gsi::arg ("d"), gsi::arg ("whole_edges", false), gsi::arg ("metrics", db::metrics_type::Euclidian, "Euclidian"), gsi::arg ("ignore_angle", tl::Variant (), "default"), gsi::arg ("min_projection", tl::Variant (), "0"), gsi::arg ("max_projection", tl::Variant (), "max"), gsi::arg ("shielded", true), gsi::arg ("opposite_filter", db::NoOppositeFilter, "NoOppositeFilter"), gsi::arg ("rect_filter", db::NoSideAllowed, "NoSideAllowed"), gsi::arg ("negative", false),
     "@brief Performs an enclosing check with options\n"
@@ -2675,7 +2687,7 @@ Class<db::Region> decl_Region (decl_dbShapeCollection, "db", "Region",
     "@param max_projection The upper limit of the projected length of one edge onto another\n"
     "@param opposite_filter Specifies a filter mode for errors happening on opposite sides of inputs shapes\n"
     "@param rect_filter Specifies an error filter for rectangular input shapes\n"
-    "@param negative If true, edges not violation the condition will be output as pseudo-edge pairs\n"
+    "@param negative Negative output from the first input\n"
     "\n"
     "If \"whole_edges\" is true, the resulting \\EdgePairs collection will receive the whole "
     "edges which contribute in the width check.\n"
@@ -2703,9 +2715,15 @@ Class<db::Region> decl_Region (decl_dbShapeCollection, "db", "Region",
     "\"opposite_filter\" specifies whether to require or reject errors happening on opposite sides of a figure. "
     "\"rect_filter\" allows suppressing specific error configurations on rectangular input figures.\n"
     "\n"
+    "If \"negative\" is true, only edges from the first input are output as pseudo edge-pairs where the enclosure is "
+    "larger or equal to the limit. This is a way to flag the parts of the first input where the enclosure vs. the second "
+    "input is bigger. Note that only the first input's edges are output. The output is still edge pairs, but each edge pair "
+    "contains one edge from the original input and the reverse version of the edge as the second edge.\n"
+    "\n"
     "Merged semantics applies for the input of this method (see \\merged_semantics= for a description of this concept)\n"
     "\n"
-    "The 'shielded', 'negative', 'not_opposite' and 'rect_sides' options have been introduced in version 0.27."
+    "The 'shielded', 'negative', 'not_opposite' and 'rect_sides' options have been introduced in version 0.27. "
+    "The interpretation of the 'negative' flag has been restriced to first-layout only output in 0.27.1.\n"
   ) +
   method_ext ("separation_check", &separation2, gsi::arg ("other"), gsi::arg ("d"), gsi::arg ("whole_edges", false), gsi::arg ("metrics", db::metrics_type::Euclidian, "Euclidian"), gsi::arg ("ignore_angle", tl::Variant (), "default"), gsi::arg ("min_projection", tl::Variant (), "0"), gsi::arg ("max_projection", tl::Variant (), "max"), gsi::arg ("shielded", true), gsi::arg ("opposite_filter", db::NoOppositeFilter, "NoOppositeFilter"), gsi::arg ("rect_filter", db::NoSideAllowed, "NoSideAllowed"), gsi::arg ("negative", false),
     "@brief Performs a separation check with options\n"
@@ -2718,7 +2736,7 @@ Class<db::Region> decl_Region (decl_dbShapeCollection, "db", "Region",
     "@param max_projection The upper limit of the projected length of one edge onto another\n"
     "@param opposite_filter Specifies a filter mode for errors happening on opposite sides of inputs shapes\n"
     "@param rect_filter Specifies an error filter for rectangular input shapes\n"
-    "@param negative If true, edges not violation the condition will be output as pseudo-edge pairs\n"
+    "@param negative Negative output from the first input\n"
     "\n"
     "If \"whole_edges\" is true, the resulting \\EdgePairs collection will receive the whole "
     "edges which contribute in the width check.\n"
@@ -2746,9 +2764,15 @@ Class<db::Region> decl_Region (decl_dbShapeCollection, "db", "Region",
     "\"opposite_filter\" specifies whether to require or reject errors happening on opposite sides of a figure. "
     "\"rect_filter\" allows suppressing specific error configurations on rectangular input figures.\n"
     "\n"
+    "If \"negative\" is true, only edges from the first input are output as pseudo edge-pairs where the separation is "
+    "larger or equal to the limit. This is a way to flag the parts of the first input where the distance to the second "
+    "input is bigger. Note that only the first input's edges are output. The output is still edge pairs, but each edge pair "
+    "contains one edge from the original input and the reverse version of the edge as the second edge.\n"
+    "\n"
     "Merged semantics applies for the input of this method (see \\merged_semantics= for a description of this concept)\n"
     "\n"
-    "The 'shielded', 'negative', 'not_opposite' and 'rect_sides' options have been introduced in version 0.27."
+    "The 'shielded', 'negative', 'not_opposite' and 'rect_sides' options have been introduced in version 0.27. "
+    "The interpretation of the 'negative' flag has been restriced to first-layout only output in 0.27.1.\n"
   ) +
   method_ext ("area", &area1,
     "@brief The area of the region\n"
diff --git a/src/drc/unit_tests/drcSimpleTests.cc b/src/drc/unit_tests/drcSimpleTests.cc
index aef50bbde..b4d065902 100644
--- a/src/drc/unit_tests/drcSimpleTests.cc
+++ b/src/drc/unit_tests/drcSimpleTests.cc
@@ -1272,3 +1272,13 @@ TEST(47_fillWithOverlappingBoxesTiled)
 {
   run_test (_this, "47", false);
 }
+
+TEST(48_drcWithFragments)
+{
+  run_test (_this, "48", false);
+}
+
+TEST(48d_drcWithFragments)
+{
+  run_test (_this, "48", true);
+}
diff --git a/testdata/drc/drcSimpleTests_48.drc b/testdata/drc/drcSimpleTests_48.drc
new file mode 100644
index 000000000..672fe9270
--- /dev/null
+++ b/testdata/drc/drcSimpleTests_48.drc
@@ -0,0 +1,44 @@
+
+source $drc_test_source
+target $drc_test_target
+
+if $drc_test_deep
+  deep
+end
+
+l1 = input(1, 0)
+l2 = input(2, 0)
+
+l1.output(1, 0)
+l2.output(2, 0)
+
+l1.drc(separation(l2, projection) < 1.0).output(100, 0)
+l1.drc(separation(l2, whole_edges, projection) < 1.0).output(101, 0)
+l1.drc(separation(l2, projection) >= 1.0).output(102, 0)
+l1.separation(l2, projection, 1.0).output(110, 0)
+l1.separation(l2, projection, 1.0, whole_edges).output(111, 0)
+
+l2.drc(separation(l1, projection) < 1.0).output(200, 0)
+l2.drc(separation(l1, whole_edges, projection) < 1.0).output(201, 0)
+l2.drc(separation(l1, projection) >= 1.0).output(202, 0)
+l2.separation(l1, projection, 1.0).output(210, 0)
+l2.separation(l1, projection, 1.0, whole_edges).output(211, 0)
+
+(l1 + l2).drc(space(projection) < 1.0).output(300, 0)
+(l1 + l2).drc(space(whole_edges, projection) < 1.0).output(301, 0)
+(l1 + l2).drc(space(projection) >= 1.0).output(302, 0)
+(l1 + l2).space(projection, 1.0).output(310, 0)
+(l1 + l2).space(projection, 1.0, whole_edges).output(311, 0)
+
+l1.drc(enclosing(l2, projection) < 1.0).output(400, 0)
+l1.drc(enclosing(l2, whole_edges, projection) < 1.0).output(401, 0)
+l1.drc(enclosing(l2, projection) >= 1.0).output(402, 0)
+l1.enclosing(l2, projection, 1.0).output(410, 0)
+l1.enclosing(l2, projection, 1.0, whole_edges).output(411, 0)
+
+l1.drc(overlap(l2, projection) < 1.0).output(500, 0)
+l1.drc(overlap(l2, whole_edges, projection) < 1.0).output(501, 0)
+l1.drc(overlap(l2, projection) >= 1.0).output(502, 0)
+l1.overlap(l2, projection, 1.0).output(510, 0)
+l1.overlap(l2, projection, 1.0, whole_edges).output(511, 0)
+
diff --git a/testdata/drc/drcSimpleTests_48.gds b/testdata/drc/drcSimpleTests_48.gds
new file mode 100644
index 000000000..8742b1c65
Binary files /dev/null and b/testdata/drc/drcSimpleTests_48.gds differ
diff --git a/testdata/drc/drcSimpleTests_au48.gds b/testdata/drc/drcSimpleTests_au48.gds
new file mode 100644
index 000000000..4f81f169a
Binary files /dev/null and b/testdata/drc/drcSimpleTests_au48.gds differ