diff --git a/main/src/main/scala/sbt/Cross.scala b/main/src/main/scala/sbt/Cross.scala
index c6aafaa9d..6d426b95e 100644
--- a/main/src/main/scala/sbt/Cross.scala
+++ b/main/src/main/scala/sbt/Cross.scala
@@ -41,6 +41,12 @@ object Cross {
         case _           => ("", arg)
       }
       val home = IO.resolve(x.currentProject.base, new File(homePath))
+      // Basic Algorithm.
+      // 1. First we figure out what the new scala instances should be, create settings for them.
+      // 2. Find any non-overridden scalaVersion setting in the whole build and force it to delegate
+      //    to the new global settings.
+      // 3. Append these to the session, so that the session is up-to-date and
+      //    things like set/session clear, etc. work.
       val (add, exclude) =
         if (home.exists) {
           val instance = ScalaInstance(home)(state.classLoaderCache.apply _)
@@ -63,10 +69,18 @@ object Cross {
           )
           (settings, excludeKeys(Set(scalaVersion.key, scalaHome.key)))
         }
-      val cleared = session.mergeSettings.filterNot(exclude)
-      val newStructure = Load.reapply(add ++ cleared, structure)
-      Project.setProject(session, newStructure, command :: state)
+      // TODO - Track delegates and avoid regenerating.
+      val delegates: Seq[Setting[_]] = session.mergeSettings collect {
+        case x if exclude(x) => delegateToGlobal(x.key)
+      }
+      val fixedSession = session.appendRaw(add ++ delegates)
+      BuiltinCommands.reapply(fixedSession, structure, state)
   }
+
+  // Creates a delegate for a scoped key that pulls the setting from the global scope.
+  private[this] def delegateToGlobal[T](key: ScopedKey[T]): Setting[_] =
+    SettingKey[T](key.key) in key.scope := (SettingKey[T](key.key) in GlobalScope).value
+
   @deprecated("No longer used.", "0.13.0")
   def crossExclude(s: Setting[_]): Boolean = excludeKeys(Set(scalaVersion.key, scalaHome.key))(s)
 
diff --git a/notes/0.13.6.md b/notes/0.13.6.md
index a35f51ff1..48fcf27aa 100644
--- a/notes/0.13.6.md
+++ b/notes/0.13.6.md
@@ -1,4 +1,5 @@
   [413]: https://github.com/sbt/sbt/issues/413
+  [856]: https://github.com/sbt/sbt/issues/856
   [1036]: https://github.com/sbt/sbt/pull/1036
   [1059]: https://github.com/sbt/sbt/issues/1059
   [1194]: https://github.com/sbt/sbt/issues/1194
@@ -36,6 +37,8 @@
   [1486]: https://github.com/sbt/sbt/pull/1486
   [1487]: https://github.com/sbt/sbt/pull/1487
   [1488]: https://github.com/sbt/sbt/pull/1488
+  [1489]: https://github.com/sbt/sbt/pull/1489
+
   [@dansanduleac]: https://github.com/dansanduleac
   [@2m]: https://github.com/2m
   [@pvlugter]: https://github.com/pvlugter
@@ -82,6 +85,7 @@
 - Fixes sLog usage in tandem with the `set` comamnd [#1486][1486] [@jsuereth][@jsuereth]
 - Test suites with whitespace will have prettier filenames [#1487][1487] [@jsuereth][@jsuereth]
 - sbt no longer crashes when run in root directory [#1488][1488] by [@jsuereth][@jsuereth]
+- set no longer removes any `++` scala version setting.  [#856][856]/[#1489][1489] by [@jsuereth][@jsuereth]
 
 ### enablePlugins/disablePlugins
 
diff --git a/sbt/src/sbt-test/actions/cross/test b/sbt/src/sbt-test/actions/cross/test
index de92dc24c..ee74f0f8a 100644
--- a/sbt/src/sbt-test/actions/cross/test
+++ b/sbt/src/sbt-test/actions/cross/test
@@ -1,3 +1,8 @@
 > check 2.7.7 2.9.1 2.9.0-1
 > ++ 2.8.2
 > check 2.8.2 2.8.2 2.8.1
+> ++ 2.10.4
+> set resolvers ++= Nil
+> check 2.10.4 2.10.4 2.10.4
+> session clear-all
+> check 2.7.7 2.9.1 2.9.0-1
\ No newline at end of file