--- a/cnd.makeproject/src/org/netbeans/modules/cnd/makeproject/NativeProjectProvider.java	
+++ a/cnd.makeproject/src/org/netbeans/modules/cnd/makeproject/NativeProjectProvider.java	
@@ -343,11 +343,13 @@ 
             if (nativeFileIetm == null) {
                 continue;
             }
-            PredefinedToolKind tool = ((Item) nativeFileIetm).getDefaultTool();
-            if (tool == PredefinedToolKind.CustomTool
-                    // check of mime type is better to support headers without extensions
-                    && !MIMENames.HEADER_MIME_TYPE.equals(((Item) nativeFileIetm).getMIMEType())) {
-                continue; // IZ 87407
+            if (nativeFileIetm instanceof Item) {
+                PredefinedToolKind tool = ((Item) nativeFileIetm).getDefaultTool();
+                if (tool == PredefinedToolKind.CustomTool
+                        // check of mime type is better to support headers without extensions
+                        && !MIMENames.HEADER_MIME_TYPE.equals(((Item) nativeFileIetm).getMIMEType())) {
+                    continue; // IZ 87407
+                }
             }
             actualList.add(nativeFileIetm);
             if (TRACE) {
@@ -1278,7 +1280,7 @@ 
         }
     }
     
-    private static class NativeFileIndexer implements NativeFileItem {
+    public static class NativeFileIndexer implements NativeFileItem {
 
         private final FileObject indexer;
         private final NativeFileItem.Language language;
@@ -1357,5 +1359,31 @@ 
         public boolean isExcluded() {
             return false;
         }
+
+        public int getCRC() {
+        int res = 0;
+        for(IncludePath aPath : getUserIncludePaths()) {
+            res += 37 * aPath.getFSPath().hashCode();
+        }
+        for(FSPath aPath : getIncludeFiles()) {
+            res += 37 * aPath.hashCode();
+        }
+        for(String macro: getUserMacroDefinitions()) {
+            res += 37 * macro.hashCode();
+        }
+        for(IncludePath aPath : getSystemIncludePaths()) {
+            res += 37 * aPath.getFSPath().hashCode();
+        }
+        for(FSPath aPath : getSystemIncludeHeaders()) {
+            res += 37 * aPath.getPath().hashCode();
+        }
+        for(String macro: getSystemMacroDefinitions()) {
+            res += 37 * macro.hashCode();
+        }
+        res += 37 * getLanguage().hashCode();
+        res += 37 * getLanguageFlavor().hashCode();
+        return res;
+    }
+
     }
 }
--- a/cnd.makeproject/src/org/netbeans/modules/cnd/makeproject/api/configurations/ConfigurationDescriptorProvider.java	
+++ a/cnd.makeproject/src/org/netbeans/modules/cnd/makeproject/api/configurations/ConfigurationDescriptorProvider.java	
@@ -56,8 +56,10 @@ 
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.netbeans.api.project.Project;
+import org.netbeans.modules.cnd.api.project.NativeFileItem;
 import org.netbeans.modules.cnd.api.toolchain.CompilerSet;
 import org.netbeans.modules.cnd.makeproject.MakeProjectImpl;
+import org.netbeans.modules.cnd.makeproject.NativeProjectProvider;
 import org.netbeans.modules.cnd.makeproject.api.configurations.ConfigurationDescriptor.State;
 import org.netbeans.modules.cnd.makeproject.configurations.ConfigurationXMLReader;
 import org.netbeans.modules.cnd.makeproject.uiapi.ConfirmSupport;
@@ -566,50 +568,42 @@ 
     public static final class Delta implements SnapShot {
 
         private final Map<String, Pair> oldState = new HashMap<>();
-        private final List<Item> included = new ArrayList<>();
-        private final List<Item> added = new ArrayList<>(); 
-        private final List<Item> excluded = new ArrayList<>(); 
-        private final List<Item> deleted = new ArrayList<>(); 
-        private final List<Item> changed = new ArrayList<>(); 
-        private final List<Item> replaced = new ArrayList<>(); 
+        private final List<NativeFileItem> included = new ArrayList<>();
+        private final List<NativeFileItem> added = new ArrayList<>(); 
+        private final List<NativeFileItem> excluded = new ArrayList<>(); 
+        private final List<NativeFileItem> deleted = new ArrayList<>(); 
+        private final List<NativeFileItem> changed = new ArrayList<>(); 
+        private final List<NativeFileItem> replaced = new ArrayList<>(); 
 
         private Delta(MakeConfigurationDescriptor oldDescriptor) {
             if (oldDescriptor != null) {
                 for(Item item : oldDescriptor.getProjectItems()) {
                     oldState.put(item.getAbsolutePath(), new Pair(item, item.getCRC(), item.isExcluded()));
                 }
+                NativeProjectProvider np = oldDescriptor.getProject().getLookup().lookup(NativeProjectProvider.class);
+                for(NativeFileItem item : np.getStandardHeadersIndexers()) {
+                    if (item instanceof NativeProjectProvider.NativeFileIndexer) {
+                        NativeProjectProvider.NativeFileIndexer indexer = (NativeProjectProvider.NativeFileIndexer)item;
+                        oldState.put(item.getAbsolutePath(), new Pair(indexer, indexer.getCRC(), indexer.isExcluded()));
+                    }
+                }
             }
         }
         
         private void computeDelta(MakeConfigurationDescriptor newDescriptor) {
-            Set<Item> oldSet = new HashSet<>();
+            Set<NativeFileItem> oldSet = new HashSet<>();
             oldState.entrySet().forEach((entry) -> {
                 oldSet.add(entry.getValue().item);
             });
             Item[] newItems = newDescriptor.getProjectItems();
             for (Item item : newItems) {
-                Delta.Pair pair = oldState.get(item.getAbsolutePath());
-                if (pair == null) {
-                    added.add(item);
-                } else {
-                    oldSet.remove(pair.item);
-                    if (item.isExcluded() && pair.excluded) {
-                        // no changes
-                        replaced.add(item);
-                    } else if (item.isExcluded() && !pair.excluded) {
-                        excluded.add(item);
-                    } else if (!item.isExcluded() && pair.excluded) {
-                        included.add(item);
-                    } else {
-                        // compare item properties
-                        if (item.getCRC() != pair.crc) {
-                            changed.add(item);
-                        } else {
-                            if (pair.item != item) {
-                                replaced.add(item);
-                            }
-                        }
-                    }
+                checkItem(item, oldSet, item.getCRC());
+            }
+            NativeProjectProvider np = newDescriptor.getProject().getLookup().lookup(NativeProjectProvider.class);
+            for(NativeFileItem item : np.getStandardHeadersIndexers()) {
+                if (item instanceof NativeProjectProvider.NativeFileIndexer) {
+                    NativeProjectProvider.NativeFileIndexer indexer = (NativeProjectProvider.NativeFileIndexer)item;
+                    checkItem(indexer, oldSet, indexer.getCRC());
                 }
             }
             oldSet.forEach((item) -> {
@@ -617,6 +611,32 @@ 
             });
             oldState.clear();
         }
+
+        private void checkItem(NativeFileItem item, Set<NativeFileItem> oldSet, int itemCRC) {
+            Delta.Pair pair = oldState.get(item.getAbsolutePath());
+            if (pair == null) {
+                added.add(item);
+            } else {
+                oldSet.remove(pair.item);
+                if (item.isExcluded() && pair.excluded) {
+                    // no changes
+                    replaced.add(item);
+                } else if (item.isExcluded() && !pair.excluded) {
+                    excluded.add(item);
+                } else if (!item.isExcluded() && pair.excluded) {
+                    included.add(item);
+                } else {
+                    // compare item properties
+                    if (itemCRC != pair.crc) {
+                        changed.add(item);
+                    } else {
+                        if (pair.item != item) {
+                            replaced.add(item);
+                        }
+                    }
+                }
+            }
+        }
         
         public void printStatistic(Logger logger) {
             if (logger.isLoggable(CndUtils.isUnitTestMode()? Level.FINE : Level.INFO)) {
@@ -632,50 +652,50 @@ 
         /**
          * marked as included items
          */
-        public List<Item> getIncluded() {
+        public List<NativeFileItem> getIncluded() {
             return Collections.unmodifiableList(included);
         }
 
         /**
          * added in project items
          */
-        public List<Item> getAdded() {
+        public List<NativeFileItem> getAdded() {
             return Collections.unmodifiableList(added);
         }
 
         /**
          * marked as excluded items
          */
-        public List<Item> getExcluded() {
+        public List<NativeFileItem> getExcluded() {
             return Collections.unmodifiableList(excluded);
         }
 
         /**
          * deleted from project items
          */
-        public List<Item> getDeleted() {
+        public List<NativeFileItem> getDeleted() {
             return Collections.unmodifiableList(deleted);
         }
 
         /**
          * items with changed properties
          */
-        public List<Item> getChanged() {
+        public List<NativeFileItem> getChanged() {
             return Collections.unmodifiableList(changed);
         }
 
         /**
          * Items which properties were not changed (from code model point of view) but instances were replaced
          */
-        public List<Item> getReplaced() {
+        public List<NativeFileItem> getReplaced() {
             return Collections.unmodifiableList(replaced);
         }
         
         private static final class Pair {
             final int crc;
             final boolean excluded;
-            final Item item;
-            private Pair(Item item, int crc, boolean excluded) {
+            final NativeFileItem item;
+            private Pair(NativeFileItem item, int crc, boolean excluded) {
                 this.crc = crc;
                 this.excluded = excluded;
                 this.item = item;
--- a/cnd.makeproject/src/org/netbeans/modules/cnd/makeproject/api/configurations/MakeConfigurationDescriptor.java	
+++ a/cnd.makeproject/src/org/netbeans/modules/cnd/makeproject/api/configurations/MakeConfigurationDescriptor.java	
@@ -972,21 +972,21 @@ 
         if (delta.isEmpty()) {
             return;
         }
-        List<Item> deleted = delta.getDeleted();
-        List<Item> excluded = delta.getExcluded();
+        List<NativeFileItem> deleted = delta.getDeleted();
+        List<NativeFileItem> excluded = delta.getExcluded();
         if (!(deleted.isEmpty() && excluded.isEmpty())) {
             List<NativeFileItem> list = new ArrayList<NativeFileItem>(deleted);
             list.addAll(excluded);
             getNativeProjectChangeSupport().fireFilesRemoved(list);
         }
-        List<Item> added = delta.getAdded();
-        List<Item> included = delta.getIncluded();
+        List<NativeFileItem> added = delta.getAdded();
+        List<NativeFileItem> included = delta.getIncluded();
         if (!(added.isEmpty() && included.isEmpty())) {
             List<NativeFileItem> list = new ArrayList<NativeFileItem>(added);
             list.addAll(included);
             getNativeProjectChangeSupport().fireFilesAdded(list);
         }
-        List<Item> changed = delta.getChanged();
+        List<NativeFileItem> changed = delta.getChanged();
         if (!changed.isEmpty()) {
             getNativeProjectChangeSupport().fireFilesPropertiesChanged(new ArrayList<NativeFileItem>(changed));
         }