diff --git a/main/src/main/scala/sbt/internal/server/BuildServerReporter.scala b/main/src/main/scala/sbt/internal/server/BuildServerReporter.scala
index 5b25d17b0..b4ef0d320 100644
--- a/main/src/main/scala/sbt/internal/server/BuildServerReporter.scala
+++ b/main/src/main/scala/sbt/internal/server/BuildServerReporter.scala
@@ -25,6 +25,7 @@ import xsbti.{
 
 import scala.collection.JavaConverters._
 import scala.collection.mutable
+import java.nio.file.Path
 
 /**
 Provides methods for sending success and failure reports and publishing diagnostics.
@@ -90,7 +91,7 @@ final class BuildServerReporterImpl(
   import sbt.internal.inc.JavaInterfaceUtil._
 
   private lazy val exchange = StandardMain.exchange
-  private val problemsByFile = mutable.Map[VirtualFileRef, Vector[Problem]]()
+  private val problemsByFile = mutable.Map[Path, Vector[Problem]]()
 
   // sometimes the compiler returns a fake position such as <macro>
   // on Windows, this causes InvalidPathException (see #5994 and #6720)
@@ -114,9 +115,10 @@ final class BuildServerReporterImpl(
 
   override def sendFailureReport(sources: Array[VirtualFile]): Unit = {
     for (source <- sources) {
-      val problems = problemsByFile.getOrElse(source, Vector.empty)
+      val problems = problemsByFile.getOrElse(converter.toPath(source), Vector.empty)
       sendReport(source, problems)
     }
+    notifyFirstReport()
   }
 
   private def sendReport(source: VirtualFileRef, problems: Vector[Problem]): Unit = {
@@ -153,7 +155,11 @@ final class BuildServerReporterImpl(
       id <- problem.position.sourcePath.toOption
       (document, diagnostic) <- mapProblemToDiagnostic(problem)
     } {
-      val fileRef = VirtualFileRef.of(id)
+      // Note: We're putting the real path in `fileRef` because the `id` String can take
+      // two forms, either a ${something}/relativePath, or the absolute path of the source.
+      // But where we query this, we always have _only_ a ${something}/relativePath available.
+      // So here we "normalize" to the real path.
+      val fileRef = converter.toPath(VirtualFileRef.of(id))
       problemsByFile(fileRef) = problemsByFile.getOrElse(fileRef, Vector.empty) :+ problem
 
       val params = PublishDiagnosticsParams(
diff --git a/server-test/src/test/scala/testpkg/BuildServerTest.scala b/server-test/src/test/scala/testpkg/BuildServerTest.scala
index fff085a94..d30c9f1e7 100644
--- a/server-test/src/test/scala/testpkg/BuildServerTest.scala
+++ b/server-test/src/test/scala/testpkg/BuildServerTest.scala
@@ -236,6 +236,77 @@ object BuildServerTest extends AbstractServerTest {
     )
   }
 
+  test("buildTarget/compile [Java diagnostics] clear stale warnings") { _ =>
+    val buildTarget = buildTargetUri("javaProj", "Compile")
+    val testFile = new File(svr.baseDirectory, s"java-proj/src/main/java/example/Hello.java")
+
+    val otherBuildFile = new File(svr.baseDirectory, "force-java-out-of-process-compiler.sbt")
+    // Setting `javaHome` will force SBT to shell out to an external Java compiler instead
+    // of using the local compilation service offered by the JVM running this SBT instance.
+    IO.write(
+      otherBuildFile,
+      """
+        |lazy val javaProj = project
+        |  .in(file("java-proj"))
+        |  .settings(
+        |    javacOptions += "-Xlint:all",
+        |    javaHome := Some(file(System.getProperty("java.home")))
+        |  )
+        |""".stripMargin
+    )
+    reloadWorkspace()
+
+    compile(buildTarget)
+
+    assertMessage(
+      "build/publishDiagnostics",
+      "Hello.java",
+      """"severity":2""",
+      """found raw type: List"""
+    )(message = "should send publishDiagnostics with severity 2 for Hello.java")
+
+    assertMessage(
+      "build/publishDiagnostics",
+      "Hello.java",
+      """"severity":1""",
+      """incompatible types: int cannot be converted to String"""
+    )(
+      message = "should send publishDiagnostics with severity 1 for Hello.java"
+    )
+    // Note the messages changed slightly in both cases. That's interesting…
+
+    IO.write(
+      testFile,
+      """|package example;
+         |
+         |import java.util.List;
+         |import java.util.ArrayList;
+         |
+         |class Hello {
+         |    public static void main(String[] args) {
+         |        List<String> list = new ArrayList<>();
+         |        String msg = "42";
+         |        System.out.println(msg);
+         |    }
+         |}
+         |""".stripMargin
+    )
+
+    compile(buildTarget)
+
+    assertMessage(
+      "build/publishDiagnostics",
+      "Hello.java",
+      "\"diagnostics\":[]",
+      "\"reset\":true"
+    )(
+      message = "should send publishDiagnostics with empty diagnostics"
+    )
+
+    IO.delete(otherBuildFile)
+    reloadWorkspace()
+  }
+
   test("buildTarget/scalacOptions, buildTarget/javacOptions") { _ =>
     val buildTargets = Seq(
       buildTargetUri("util", "Compile"),