diff --git a/build/org.eclipse.cdt.cmake.core/src/org/eclipse/cdt/cmake/core/internal/CMakeBuildConfiguration.java b/build/org.eclipse.cdt.cmake.core/src/org/eclipse/cdt/cmake/core/internal/CMakeBuildConfiguration.java
index be3b7aa1b16..c56396acf50 100644
--- a/build/org.eclipse.cdt.cmake.core/src/org/eclipse/cdt/cmake/core/internal/CMakeBuildConfiguration.java
+++ b/build/org.eclipse.cdt.cmake.core/src/org/eclipse/cdt/cmake/core/internal/CMakeBuildConfiguration.java
@@ -15,6 +15,7 @@ import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -231,7 +232,11 @@ public class CMakeBuildConfiguration extends CBuildConfiguration {
 			try (FileReader reader = new FileReader(commandsFile.toFile())) {
 				Gson gson = new Gson();
 				CompileCommand[] commands = gson.fromJson(reader, CompileCommand[].class);
+				Map<String, CompileCommand> dedupedCmds = new HashMap<>();
 				for (CompileCommand command : commands) {
+					dedupedCmds.put(command.getFile(), command);
+				}
+				for (CompileCommand command : dedupedCmds.values()) {
 					processLine(command.getCommand());
 				}
 				shutdown();
diff --git a/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/CBuildConfiguration.java b/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/CBuildConfiguration.java
index c3daf8b8fb2..6f6a1fb38b0 100644
--- a/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/CBuildConfiguration.java
+++ b/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/CBuildConfiguration.java
@@ -633,15 +633,18 @@ public abstract class CBuildConfiguration extends PlatformObject
 				for (IResource resource : resources) {
 					loadScannerInfoCache();
 					if (scannerInfoCache.hasCommand(commandStrings)) {
-						scannerInfoCache.addResource(commandStrings, resource);
+						if (!scannerInfoCache.hasResource(commandStrings, resource)) {
+							scannerInfoCache.addResource(commandStrings, resource);
+							infoChanged = true;
+						}
 					} else {
 						Path commandPath = findCommand(command.get(0));
 						command.set(0, commandPath.toString());
 						IExtendedScannerInfo info = getToolChain().getScannerInfo(getBuildConfiguration(),
 								command, null, resource, getBuildDirectoryURI());
 						scannerInfoCache.addScannerInfo(commandStrings, info, resource);
+						infoChanged = true;
 					}
-					infoChanged = true;
 				}
 				return true;
 			} else {
diff --git a/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/ScannerInfoCache.java b/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/ScannerInfoCache.java
index 81f9ee74b7c..d055ce85f8b 100644
--- a/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/ScannerInfoCache.java
+++ b/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/ScannerInfoCache.java
@@ -77,7 +77,7 @@ public class ScannerInfoCache {
 				oldCommand.resourcePaths.remove(resourcePath);
 				if (oldCommand.resourcePaths.isEmpty()) {
 					// unused, remove
-					commandMap.remove(commandStrings);
+					commandMap.remove(oldCommand.command);
 					commands.remove(oldCommand);
 					resourceMap.remove(resourcePath);
 				}
@@ -101,6 +101,18 @@ public class ScannerInfoCache {
 		}
 	}
 
+	/**
+	 * @since 6.3
+	 */
+	public boolean hasResource(List<String> commandStrings, IResource resource) {
+		String resourcePath = resource.getLocation().toOSString();
+		Command command = commandMap.get(commandStrings);
+		if (command == null) {
+			return false;
+		}
+		return command.resourcePaths.contains(resourcePath);
+	}
+
 	public void addResource(List<String> commandStrings, IResource resource) {
 		String resourcePath = resource.getLocation().toOSString();
 		Command command = commandMap.get(commandStrings);