Index: oak-core/src/main/java/org/apache/jackrabbit/oak/plugins/index/IndexUpdate.java
===================================================================
--- oak-core/src/main/java/org/apache/jackrabbit/oak/plugins/index/IndexUpdate.java	(revision 1845889)
+++ oak-core/src/main/java/org/apache/jackrabbit/oak/plugins/index/IndexUpdate.java	(working copy)
@@ -61,6 +61,7 @@
 import org.apache.jackrabbit.oak.spi.state.NodeBuilder;
 import org.apache.jackrabbit.oak.spi.state.NodeState;
 import org.apache.jackrabbit.oak.spi.state.NodeStateUtils;
+import org.apache.jackrabbit.oak.spi.state.ReadOnlyBuilder;
 import org.apache.jackrabbit.util.ISO8601;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -318,7 +319,12 @@
             if (NodeStateUtils.isHidden(rm)) {
                 NodeBuilder childNode = definition.getChildNode(rm);
                 if (!childNode.getBoolean(IndexConstants.REINDEX_RETAIN)) {
-                    definition.getChildNode(rm).remove();
+                    NodeBuilder child = definition.getChildNode(rm);
+                    if (child instanceof ReadOnlyBuilder) {
+                        log.debug("Preserve read-only child node on reindex: " + rm);
+                    } else {
+                        child.remove();
+                    }
                 }
             }
         }
Index: oak-lucene/src/main/java/org/apache/jackrabbit/oak/plugins/index/lucene/directory/OakDirectory.java
===================================================================
--- oak-lucene/src/main/java/org/apache/jackrabbit/oak/plugins/index/lucene/directory/OakDirectory.java	(revision 1845889)
+++ oak-lucene/src/main/java/org/apache/jackrabbit/oak/plugins/index/lucene/directory/OakDirectory.java	(working copy)
@@ -36,6 +36,7 @@
 import org.apache.jackrabbit.oak.plugins.index.search.FulltextIndexConstants;
 import org.apache.jackrabbit.oak.spi.blob.GarbageCollectableBlobStore;
 import org.apache.jackrabbit.oak.spi.state.NodeBuilder;
+import org.apache.jackrabbit.oak.spi.state.ReadOnlyBuilder;
 import org.apache.lucene.store.Directory;
 import org.apache.lucene.store.IOContext;
 import org.apache.lucene.store.IndexInput;
@@ -174,7 +175,11 @@
         } else {
             LOG.debug("Not marking {} under {} for active deletion", name, indexName);
         }
-        f.remove();
+        if (f instanceof ReadOnlyBuilder) {
+            LOG.debug("Preserve read-only node: " + name);
+        } else {
+            f.remove();
+        }
         markDirty();
     }
 
@@ -253,7 +258,11 @@
     public void close() throws IOException {
         if (!readOnly && definition.saveDirListing()) {
             if (!fileNamesAtStart.equals(fileNames)) {
-                directoryBuilder.setProperty(createProperty(PROP_DIR_LISTING, fileNames, STRINGS));
+                if (directoryBuilder instanceof ReadOnlyBuilder) {
+                    LOG.debug("Preserve files of read-only directory: " + fileNames);
+                } else {
+                    directoryBuilder.setProperty(createProperty(PROP_DIR_LISTING, fileNames, STRINGS));
+                }
             }
         }
     }
@@ -296,12 +305,16 @@
         NodeBuilder file = directoryBuilder.getChildNode(name);
         if (file.exists()) {
             // overwrite potentially already existing child
-            NodeBuilder destFile = dest.directoryBuilder.setChildNode(name, EMPTY_NODE);
-            for (PropertyState p : file.getProperties()) {
-                destFile.setProperty(p);
+            if (dest.directoryBuilder instanceof ReadOnlyBuilder) {
+                LOG.debug("Preserve read-only child: " + name);
+            } else {
+                NodeBuilder destFile = dest.directoryBuilder.setChildNode(name, EMPTY_NODE);
+                for (PropertyState p : file.getProperties()) {
+                    destFile.setProperty(p);
+                }
+                dest.fileNames.add(name);
+                dest.markDirty();
             }
-            dest.fileNames.add(name);
-            dest.markDirty();
         }
     }
 
Index: oak-store-composite/src/main/java/org/apache/jackrabbit/oak/composite/CompositeNodeBuilder.java
===================================================================
--- oak-store-composite/src/main/java/org/apache/jackrabbit/oak/composite/CompositeNodeBuilder.java	(revision 1847115)
+++ oak-store-composite/src/main/java/org/apache/jackrabbit/oak/composite/CompositeNodeBuilder.java	(working copy)
@@ -25,12 +25,13 @@
 import org.apache.jackrabbit.oak.plugins.memory.MemoryNodeBuilder;
 import org.apache.jackrabbit.oak.spi.state.NodeBuilder;
 import org.apache.jackrabbit.oak.spi.state.NodeState;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.List;
 
-import static com.google.common.base.Preconditions.checkState;
 import static java.lang.Long.MAX_VALUE;
 import static java.util.Collections.singleton;
 import static org.apache.jackrabbit.oak.composite.CompositeNodeState.STOP_COUNTING_CHILDREN;
@@ -40,6 +41,8 @@
 
 class CompositeNodeBuilder implements NodeBuilder {
 
+    private final static Logger LOG = LoggerFactory.getLogger(CompositeNodeBuilder.class);
+
     private final CompositionContext ctx;
 
     private final NodeMap<NodeBuilder> nodeBuilders;
@@ -227,9 +230,14 @@
             throw new IllegalStateException("This builder does not exist: " + PathUtils.getName(getPath()));
         }
         String childPath = simpleConcat(getPath(), name);
-        final MountedNodeStore childStore = ctx.getOwningStore(childPath);
+        MountedNodeStore childStore = ctx.getOwningStore(childPath);
         if (childStore != ctx.getGlobalStore() && !nodeBuilders.get(childStore).exists()) {
-            throw new IllegalStateException("The mount root doesn't exist: " + getPath() + " for " + childStore);
+            // if it doesn't exist in the read-only repository, create it in the global repository
+            // (needed for example for a new index)
+            if (LOG.isDebugEnabled()) {
+                LOG.debug("Creating node in the global store; will become invisible once overlayed: " + childPath);
+            }
+            childStore = ctx.getGlobalStore();
         }
         final NodeBuilder childBuilder = nodeBuilders.get(childStore).setChildNode(name, nodeState);
         if (!ctx.shouldBeComposite(childPath)) {