diff --git a/resources/bundles/org.eclipse.core.resources/src/org/eclipse/core/internal/resources/Project.java b/resources/bundles/org.eclipse.core.resources/src/org/eclipse/core/internal/resources/Project.java
index 7d18057e692..88c0bbe99da 100644
--- a/resources/bundles/org.eclipse.core.resources/src/org/eclipse/core/internal/resources/Project.java
+++ b/resources/bundles/org.eclipse.core.resources/src/org/eclipse/core/internal/resources/Project.java
@@ -22,6 +22,7 @@
 
 import java.net.URI;
 import java.util.*;
+import java.util.function.Consumer;
 import org.eclipse.core.filesystem.*;
 import org.eclipse.core.internal.events.LifecycleEvent;
 import org.eclipse.core.internal.preferences.EclipsePreferences;
@@ -199,6 +200,11 @@ public void close(IProgressMonitor monitor) throws CoreException {
 			workspace.broadcastEvent(LifecycleEvent.newEvent(LifecycleEvent.PRE_PROJECT_CLOSE, this));
 			// flush the build order early in case there is a problem
 			workspace.flushBuildOrder();
+			// Clear the linked flag of linked resources,
+			// since changes to the links in .project while the project is closed
+			// are otherwise not reflected after re-opening the project.
+			// See: https://github.com/eclipse-platform/eclipse.platform/issues/470
+			clearLinkFlags();
 			IProgressMonitor sub = subMonitor.newChild(49, SubMonitor.SUPPRESS_SUBTASK);
 			IStatus saveStatus = workspace.getSaveManager().save(ISaveContext.PROJECT_SAVE, this, sub);
 			internalClose(subMonitor.newChild(49));
@@ -1107,6 +1113,9 @@ public void open(int updateFlags, IProgressMonitor monitor) throws CoreException
 					writeEncodingAfterOpen(monitor);
 					encodingWritten = true;
 				}
+				if (used) {
+					setLinkFlags();
+				}
 				//creation of this project may affect overlapping resources
 				workspace.getAliasManager().updateAliases(this, getStore(), IResource.DEPTH_INFINITE, monitor);
 			} catch (OperationCanceledException e) {
@@ -1443,6 +1452,36 @@ public String getDefaultLineSeparator() {
 		return System.lineSeparator();
 	}
 
+	/**
+	 * Clears the {@link ICoreConstants#M_LINK} flag of linked resources.
+	 */
+	private void clearLinkFlags() {
+		modifyLinksResourceInfo(info -> info.clear(M_LINK));
+	}
+
+	/**
+	 * Sets the {@link ICoreConstants#M_LINK} flag of linked resources.
+	 */
+	private void setLinkFlags() {
+		modifyLinksResourceInfo(info -> info.set(M_LINK));
+	}
+
+	private void modifyLinksResourceInfo(Consumer<ResourceInfo> operation) {
+		ProjectDescription description = internalGetDescription();
+		HashMap<IPath, LinkDescription> linkDescriptions = description.linkDescriptions;
+		if (linkDescriptions != null) {
+			for (LinkDescription linkDescription : linkDescriptions.values()) {
+				IFile linkFile = getFile(linkDescription.getProjectRelativePath());
+				if (linkFile != null) {
+					ResourceInfo linkInfo = workspace.getResourceInfo(linkFile.getFullPath(), false, true);
+					if (linkInfo != null) {
+						operation.accept(linkInfo);
+					}
+				}
+			}
+		}
+	}
+
 	private static String getLineSeparatorFromPreferences(Preferences node) {
 		try {
 			// be careful looking up for our node so not to create any nodes as side effect
diff --git a/resources/tests/org.eclipse.core.tests.resources/src/org/eclipse/core/tests/resources/AllResourcesTests.java b/resources/tests/org.eclipse.core.tests.resources/src/org/eclipse/core/tests/resources/AllResourcesTests.java
index 26a9fa9f7e1..a0efa4229f5 100644
--- a/resources/tests/org.eclipse.core.tests.resources/src/org/eclipse/core/tests/resources/AllResourcesTests.java
+++ b/resources/tests/org.eclipse.core.tests.resources/src/org/eclipse/core/tests/resources/AllResourcesTests.java
@@ -27,6 +27,7 @@
 		LinkedResourceWithPathVariableTest.class, LinkedResourceSyncMoveAndCopyTest.class, MarkerSetTest.class,
 		MarkerTest.class, NatureTest.class, NonLocalLinkedResourceTest.class, ProjectEncodingTest.class,
 		ProjectOrderTest.class,
+		ProjectLinksTest.class,
 		ProjectScopeTest.class, ProjectSnapshotTest.class, ResourceAttributeTest.class, ResourceURLTest.class,
 		TeamPrivateMemberTest.class, WorkspaceTest.class })
 public class AllResourcesTests {
diff --git a/resources/tests/org.eclipse.core.tests.resources/src/org/eclipse/core/tests/resources/ProjectLinksTest.java b/resources/tests/org.eclipse.core.tests.resources/src/org/eclipse/core/tests/resources/ProjectLinksTest.java
new file mode 100644
index 00000000000..15a16f9c3e0
--- /dev/null
+++ b/resources/tests/org.eclipse.core.tests.resources/src/org/eclipse/core/tests/resources/ProjectLinksTest.java
@@ -0,0 +1,102 @@
+/*******************************************************************************
+ * Copyright (c) 2023 Simeon Andreev and others.
+ *
+ * This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License 2.0
+ * which accompanies this distribution, and is available at
+ * https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ *
+ * Contributors:
+ *     Simeon Andreev - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.core.tests.resources;
+
+import java.nio.file.*;
+import java.util.List;
+import org.eclipse.core.resources.*;
+import org.eclipse.core.runtime.IPath;
+
+/**
+ *
+ */
+public class ProjectLinksTest extends ResourceTest {
+
+	private IProject project;
+	private Path tmpFolder;
+	private IPath tmpPath;
+
+	@Override
+	protected void setUp() throws Exception {
+		super.setUp();
+		tmpPath = getRandomLocation();
+		tmpFolder = Paths.get(tmpPath.toOSString());
+		Files.createDirectory(tmpFolder);
+
+		IWorkspaceRoot root = getWorkspace().getRoot();
+		project = root.getProject(getUniqueString());
+
+		project.create(getMonitor());
+		project.open(getMonitor());
+		project.refreshLocal(IResource.DEPTH_INFINITE, getMonitor());
+	}
+
+	@Override
+	protected void tearDown() throws Exception {
+		try {
+			Files.deleteIfExists(tmpFolder);
+			project.delete(true, getMonitor());
+		} finally {
+			super.tearDown();
+		}
+	}
+
+	/**
+	 * Tests that link information is updated after closing a project, deleting a
+	 * link in the {@code .project} file and then opening the project.
+	 */
+	public void testCloseProjectDeleteLinksAndOpen_GH470() throws Exception {
+		IFile dotProject = project.getFile(".project");
+		Path dotProjectPath = Paths.get(dotProject.getLocationURI());
+		List<String> dotProjectContentsWithoutLink = Files.readAllLines(dotProjectPath);
+
+		String linkedFolderName = "test";
+		IFolder folder = project.getFolder(linkedFolderName);
+		folder.createLink(tmpPath, IResource.NONE, getMonitor());
+		project.refreshLocal(IResource.DEPTH_INFINITE, getMonitor());
+
+		assertTrue("Failed to create linked folder in test project", folder.isLinked());
+
+		project.close(getMonitor());
+
+		Files.write(dotProjectPath, dotProjectContentsWithoutLink);
+
+		project.open(getMonitor());
+		project.refreshLocal(IResource.DEPTH_INFINITE, getMonitor());
+
+		folder = project.getFolder(linkedFolderName);
+		assertFalse("Expected folder to not be linked after re-opening project", folder.isLinked());
+	}
+
+	/**
+	 * Tests that link information is correct after closing a project and then
+	 * opening the project.
+	 */
+	public void testCloseAndOpenProject() throws Exception {
+		String linkedFolderName = "test";
+		IFolder folder = project.getFolder(linkedFolderName);
+		folder.createLink(tmpPath, IResource.NONE, getMonitor());
+		project.refreshLocal(IResource.DEPTH_INFINITE, getMonitor());
+
+		assertTrue("Failed to create linked folder in test project", folder.isLinked());
+
+		project.close(getMonitor());
+
+		project.open(getMonitor());
+		project.refreshLocal(IResource.DEPTH_INFINITE, getMonitor());
+
+		folder = project.getFolder(linkedFolderName);
+		assertTrue("Expected folder to be linked after re-opening project", folder.isLinked());
+	}
+}