diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/DocumentLifeCycleHandler.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/DocumentLifeCycleHandler.java
index 434fe1450d..a5a65cbb90 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/DocumentLifeCycleHandler.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/DocumentLifeCycleHandler.java
@@ -378,6 +378,9 @@ public void handleClosed(DidCloseTextDocumentParams params) {
 			return;
 		}
 		try {
+			synchronized (toReconcile) {
+				toReconcile.remove(unit);
+			}
 			if (JDTUtils.isDefaultProject(unit) || !JDTUtils.isOnClassPath(unit) || unit.getResource().isDerived()) {
 				new DiagnosticsHandler(connection, unit).clearDiagnostics();
 			}
diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/JDTLanguageServer.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/JDTLanguageServer.java
index 00dc2bd3f4..86abe252cc 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/JDTLanguageServer.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/JDTLanguageServer.java
@@ -418,7 +418,7 @@ private void toggleCapability(boolean enabled, String id, String capability, Obj
 	@Override
 	public void didChangeWatchedFiles(DidChangeWatchedFilesParams params) {
 		logInfo(">> workspace/didChangeWatchedFiles ");
-		WorkspaceEventsHandler handler = new WorkspaceEventsHandler(pm, client);
+		WorkspaceEventsHandler handler = new WorkspaceEventsHandler(pm, client, this.documentLifeCycleHandler);
 		handler.didChangeWatchedFiles(params);
 	}
 
diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/WorkspaceDiagnosticsHandler.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/WorkspaceDiagnosticsHandler.java
index 03e4676561..5aa8f7b74d 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/WorkspaceDiagnosticsHandler.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/WorkspaceDiagnosticsHandler.java
@@ -131,7 +131,9 @@ public boolean visit(IResourceDelta delta) throws CoreException {
 			markers = Arrays.copyOf(javaMarkers, javaMarkers.length + taskMarkers.length);
 			System.arraycopy(taskMarkers, 0, markers, javaMarkers.length, taskMarkers.length);
 			ICompilationUnit cu = (ICompilationUnit) JavaCore.create(file);
-			document = JsonRpcHelpers.toDocument(cu.getBuffer());
+			if (!cu.isWorkingCopy()) {
+				document = JsonRpcHelpers.toDocument(cu.getBuffer());
+			}
 		} // or a build file
 		else if (projectsManager.isBuildFile(file)) {
 			//all errors on that build file should be relevant
@@ -230,10 +232,12 @@ private void publishDiagnostics(List<IMarker> markers) {
 			String uri = JDTUtils.getFileURI(resource);
 			if (JavaCore.isJavaLikeFileName(file.getName())) {
 				ICompilationUnit cu = JDTUtils.resolveCompilationUnit(uri);
-				try {
-					document = JsonRpcHelpers.toDocument(cu.getBuffer());
-				} catch (JavaModelException e) {
-					JavaLanguageServerPlugin.logException("Failed to publish diagnostics.", e);
+				if (!cu.isWorkingCopy()) {
+					try {
+						document = JsonRpcHelpers.toDocument(cu.getBuffer());
+					} catch (JavaModelException e) {
+						JavaLanguageServerPlugin.logException("Failed to publish diagnostics.", e);
+					}
 				}
 			} else if (projectsManager.isBuildFile(file)) {
 				document = JsonRpcHelpers.toDocument(file);
diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/WorkspaceEventsHandler.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/WorkspaceEventsHandler.java
index 8ecbe2d533..284e42b50e 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/WorkspaceEventsHandler.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/handlers/WorkspaceEventsHandler.java
@@ -30,18 +30,22 @@
 import org.eclipse.jdt.ls.core.internal.managers.ProjectsManager;
 import org.eclipse.jdt.ls.core.internal.managers.ProjectsManager.CHANGE_TYPE;
 import org.eclipse.lsp4j.DidChangeWatchedFilesParams;
+import org.eclipse.lsp4j.DidCloseTextDocumentParams;
 import org.eclipse.lsp4j.FileChangeType;
 import org.eclipse.lsp4j.FileEvent;
 import org.eclipse.lsp4j.PublishDiagnosticsParams;
+import org.eclipse.lsp4j.TextDocumentIdentifier;
 
 public class WorkspaceEventsHandler {
 
 	private final ProjectsManager pm ;
 	private final JavaClientConnection connection;
+	private final DocumentLifeCycleHandler handler;
 
-	public WorkspaceEventsHandler(ProjectsManager projects, JavaClientConnection connection ) {
+	public WorkspaceEventsHandler(ProjectsManager projects, JavaClientConnection connection, DocumentLifeCycleHandler handler) {
 		this.pm = projects;
 		this.connection = connection;
+		this.handler = handler;
 	}
 
 	private CHANGE_TYPE toChangeType(FileChangeType vtype){
@@ -63,6 +67,7 @@ void didChangeWatchedFiles(DidChangeWatchedFilesParams param){
 			CHANGE_TYPE changeType = toChangeType(fileEvent.getType());
 			if(changeType==CHANGE_TYPE.DELETED){
 				cleanUpDiagnostics(fileEvent.getUri());
+				handler.didClose(new DidCloseTextDocumentParams(new TextDocumentIdentifier(fileEvent.getUri())));
 			}
 			ICompilationUnit unit = JDTUtils.resolveCompilationUnit(fileEvent.getUri());
 			if (unit != null && changeType == CHANGE_TYPE.CREATED && !unit.exists()) {