diff --git a/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java b/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java
index 58fd92faa26495dea0a42ae4861d319296a2e94b..b9d517959c4cf510e3df1b1ee37e1411c8dcf509 100644
--- a/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java
@@ -1108,6 +1108,8 @@ public class IndexedGFFDocumentEntry implements DocumentEntry
     this.contig = contig;
     this.combinedReference = combinedReference;
     featureCount = -1;
+    
+    gffCache.clear();
   }
 
   public void setEntryGroup(EntryGroup entryGroup)