diff --git a/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/app/BootLanguageServerInitializer.java b/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/app/BootLanguageServerInitializer.java
index f432f8299..eac98214a 100644
--- a/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/app/BootLanguageServerInitializer.java
+++ b/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/app/BootLanguageServerInitializer.java
@@ -99,7 +99,7 @@ public class BootLanguageServerInitializer implements InitializingBean {
 			
 			@Override
 			public void deleted(IJavaProject project) {
-				doNotValidateProject(project.getLocationUri());
+				doNotValidateProject(project);
 			}
 			
 			@Override
@@ -209,7 +209,7 @@ public class BootLanguageServerInitializer implements InitializingBean {
 		
 		URI uri = project.getLocationUri();
 		
-		doNotValidateProject(uri);
+		doNotValidateProject(project);
 		
 		projectReconcileRequests.put(uri, Mono.delay(Duration.ofMillis(100))
 				.publishOn(projectReconcileScheduler)
@@ -222,15 +222,18 @@ public class BootLanguageServerInitializer implements InitializingBean {
 				.subscribe());
 	}
 	
-	private void doNotValidateProject(URI uri) {
+	private void doNotValidateProject(IJavaProject project) {
 		if (configProps.isReconcileOnlyOpenedDocs()) {
 			return;
 		}
-
+		
+		URI uri = project.getLocationUri();
 		Disposable request = projectReconcileRequests.remove(uri);
 		if (request != null) {
 			request.dispose();
 		}
+		
+		projectReconciler.clear(project);
 	}
 	
 	private void handleFiles(String[] files) {
diff --git a/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/common/IJavaProjectReconcileEngine.java b/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/common/IJavaProjectReconcileEngine.java
index 29fa8446a..1737362f7 100644
--- a/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/common/IJavaProjectReconcileEngine.java
+++ b/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/common/IJavaProjectReconcileEngine.java
@@ -19,5 +19,7 @@ import org.springframework.ide.vscode.commons.util.text.TextDocument;
 public interface IJavaProjectReconcileEngine {
 
 	void reconcile(IJavaProject project, Function<TextDocument, IProblemCollector> problemCollectorFactory);
+	
+	void clear(IJavaProject project);
 
 }
diff --git a/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/java/handlers/BootJavaReconcileEngine.java b/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/java/handlers/BootJavaReconcileEngine.java
index 28fabaff8..9b87fa573 100644
--- a/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/java/handlers/BootJavaReconcileEngine.java
+++ b/headless-services/spring-boot-language-server/src/main/java/org/springframework/ide/vscode/boot/java/handlers/BootJavaReconcileEngine.java
@@ -14,6 +14,7 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.CompletableFuture;
@@ -129,14 +130,14 @@ public class BootJavaReconcileEngine implements IReconcileEngine, IJavaProjectRe
 		}
 		Stream<Path> files = IClasspathUtil.getProjectJavaSourceFolders(project.getClasspath()).flatMap(folder -> {
 			try {
-				return Files.walk(folder.toPath());
+				return Files.walk(folder.toPath()).filter(Files::isRegularFile);
 			} catch (IOException e) {
 				return Stream.empty();
 			}
 		});
-		Stream<TextDocumentIdentifier> docIds = files.filter(f -> {
-			return Files.isRegularFile(f) && f.getFileName().toString().endsWith(".java");
-		}).map(f -> new TextDocumentIdentifier(f.toUri().toString()));
+		Stream<TextDocumentIdentifier> docIds = files
+				.filter(f -> f.getFileName().toString().endsWith(".java"))
+				.map(f -> new TextDocumentIdentifier(f.toUri().toString()));
 
 		List<TextDocument> docs = docIds.filter(docId -> documents.getLatestSnapshot(docId.getUri()) == null)
 				.map(docId -> new LazyTextDocument(docId.getUri(), LanguageId.JAVA)).collect(Collectors.toList());
@@ -163,4 +164,23 @@ public class BootJavaReconcileEngine implements IReconcileEngine, IJavaProjectRe
 
 	}
 
+	@Override
+	public void clear(IJavaProject project) {
+		// Build file
+		if (project.getProjectBuild() != null && project.getProjectBuild().getBuildFile() != null) {
+			documents.publishDiagnostics(new TextDocumentIdentifier(project.getProjectBuild().getBuildFile().toString()), Collections.emptyList());
+		}
+		// Rest of the files
+		IClasspathUtil.getProjectJavaSourceFolders(project.getClasspath()).flatMap(folder -> {
+			try {
+				return Files.walk(folder.toPath()).filter(Files::isRegularFile);
+			} catch (IOException e) {
+				return Stream.empty();
+			}
+		})
+		.filter(f -> f.getFileName().toString().endsWith(".java"))
+		.forEach(p -> documents.publishDiagnostics(new TextDocumentIdentifier(p.toUri().toString()), Collections.emptyList()));
+		
+	}
+
 }