diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectImporter.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectImporter.java
index 49680e4cda..be5d0ed76f 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectImporter.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectImporter.java
@@ -172,11 +172,11 @@ public static IClasspathEntry[] resolveClassPathEntries(IJavaProject javaProject
 			}
 		}
 
-		// Sort the source paths to make the parent folders come first
+		// Sort the source paths to make the child folders come first
 		Collections.sort(sourcePaths, new Comparator<IPath>() {
 			@Override
 			public int compare(IPath path1, IPath path2) {
-				return path1.toString().compareTo(path2.toString());
+				return path1.toString().compareTo(path2.toString()) * -1;
 			}
 		});
 
@@ -191,12 +191,6 @@ public int compare(IPath path1, IPath path2) {
 					break;
 				}
 
-				if (sourceEntry.getPath().isPrefixOf(currentPath)) {
-					JavaLanguageServerPlugin.logError("Skip source path: " + currentPath.toString() + ", since its parent path is already a source path");
-					canAddToSourceEntries = false;
-					break;
-				}
-
 				if (currentPath.isPrefixOf(sourceEntry.getPath())) {
 					exclusionPatterns.add(sourceEntry.getPath().makeRelativeTo(currentPath).addTrailingSeparator());
 				}
@@ -279,17 +273,11 @@ public static List<IPath> getSourcePaths(List<String> sourcePaths, IFolder works
 
 	public static List<IPath> getExcludingPath(IJavaProject javaProject, IPath rootPath, IFolder workspaceLinkFolder) throws CoreException {
 		if (rootPath == null) {
-			PreferenceManager preferenceManager = JavaLanguageServerPlugin.getPreferencesManager();
-			if (preferenceManager == null || preferenceManager.getPreferences() == null) {
-				throw new CoreException(new Status(IStatus.ERROR, IConstants.PLUGIN_ID, "Failed to get the preferences."));
-			}
-			Collection<IPath> rootPaths = preferenceManager.getPreferences().getRootPaths();
-			Optional<IPath> belongedRootPath = rootPaths.stream().filter(root -> root.isPrefixOf(workspaceLinkFolder.getLocation())).findFirst();
-			if (belongedRootPath.isEmpty()) {
-				throw new CoreException(new Status(IStatus.ERROR, IConstants.PLUGIN_ID, "Failed to find the belonging root of the linked folder: " + workspaceLinkFolder.toString()));
-			}
+			rootPath = ProjectUtils.findBelongedWorkspaceRoot(workspaceLinkFolder.getLocation());
+		}
 
-			rootPath = belongedRootPath.get();
+		if (rootPath == null) {
+			throw new CoreException(new Status(IStatus.ERROR, IConstants.PLUGIN_ID, "Failed to find the belonging root of the linked folder: " + workspaceLinkFolder.toString()));
 		}
 
 		final IPath root = rootPath;
diff --git a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectPreferenceChangeListener.java b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectPreferenceChangeListener.java
index 7cc9d0fa5b..5870fc6380 100644
--- a/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectPreferenceChangeListener.java
+++ b/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectPreferenceChangeListener.java
@@ -47,6 +47,9 @@ public void preferencesChange(Preferences oldPreferences, Preferences newPrefere
 
 				try {
 					IFolder workspaceLinkFolder = javaProject.getProject().getFolder(ProjectUtils.WORKSPACE_LINK);
+					if (!workspaceLinkFolder.exists()) {
+						continue;
+					}
 					List<IPath> sourcePaths = InvisibleProjectImporter.getSourcePaths(newPreferences.getInvisibleProjectSourcePaths(), workspaceLinkFolder);
 					List<IPath> excludingPaths = InvisibleProjectImporter.getExcludingPath(javaProject, null, workspaceLinkFolder);
 					IPath outputPath = InvisibleProjectImporter.getOutputPath(javaProject, newPreferences.getInvisibleProjectOutputPath(), true /*isUpdate*/);
diff --git a/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectImporterTest.java b/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectImporterTest.java
index ab5dbdd316..747259944f 100644
--- a/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectImporterTest.java
+++ b/org.eclipse.jdt.ls.tests/src/org/eclipse/jdt/ls/core/internal/managers/InvisibleProjectImporterTest.java
@@ -325,8 +325,9 @@ public void testSpecifyingNestedSourcePaths() throws Exception {
 				sourcePaths.add(entry.getPath().makeRelativeTo(linkFolder.getFullPath()).toString());
 			}
 		}
-		assertEquals(1, sourcePaths.size());
+		assertEquals(2, sourcePaths.size());
 		assertTrue(sourcePaths.contains("foo"));
+		assertTrue(sourcePaths.contains("foo/bar"));
 	}
 
 	@Test