diff --git a/src/main/java/cpath/service/ConsoleApplication.java b/src/main/java/cpath/service/ConsoleApplication.java
index 5fa698a4..5523c13c 100644
--- a/src/main/java/cpath/service/ConsoleApplication.java
+++ b/src/main/java/cpath/service/ConsoleApplication.java
@@ -201,9 +201,10 @@ private void merge() {
       LOG.info("Found {}...", service.settings().mainModelFile());
     }
 
-    service.init(); // reload the model, index, blacklist if exists...
-
     if(service.getBlacklist() == null) {
+      if(service.getModel()==null) {
+        service.init();
+      }
       LOG.info("Generating the list of ubiquitous small molecules, {}...", service.settings().blacklistFile());
       //Generate the blacklist.txt to exclude/keep ubiquitous small molecules (e.g. ATP)
       //from graph query and output format converter results.
@@ -321,7 +322,9 @@ private void postmerge() throws IOException {
     writer.close();
     LOG.info("generated datasources.txt");
 
-    service.init(); // load/reload the main model, index, etc.
+    if(service.getModel() == null) {
+      service.init(); // load/reload the main model, index, etc.
+    }
 
     //this was to integrate with UniProt portal/data - to add/update their external links to PathwayCommons apps...
     LOG.info("creating the list of primary uniprot ACs...");
diff --git a/src/main/java/cpath/service/IndexImpl.java b/src/main/java/cpath/service/IndexImpl.java
index 576082fb..6f59ac86 100644
--- a/src/main/java/cpath/service/IndexImpl.java
+++ b/src/main/java/cpath/service/IndexImpl.java
@@ -477,6 +477,7 @@ public void save(Model model) {
 		commit();
 		//force refreshing the index state (for new readers)
 		refresh();
+		setModel(model);
 		LOG.info("build(), all done.");
 	}
 
diff --git a/src/main/java/cpath/service/Merger.java b/src/main/java/cpath/service/Merger.java
index 043d7ffd..7fea893f 100644
--- a/src/main/java/cpath/service/Merger.java
+++ b/src/main/java/cpath/service/Merger.java
@@ -85,6 +85,7 @@ public void merge() {
 		log.info("Merged, saved.");
 		log.info("Indexing...");
 		service.index().save(m); // create or update all the biopax elements index
+		service.setModel(m);
 	}
 
 	//remove bad unification and relationship xrefs, if any;