Index: src/xfer.c
==================================================================
--- src/xfer.c
+++ src/xfer.c
@@ -700,11 +700,12 @@
         blob_appendf(&deleteWhere, ",%d", rid);
       }
     }
     db_finalize(&q);
     db_multi_exec(
-      "DELETE FROM unclustered WHERE rid NOT IN (0 %s)",
+      "DELETE FROM unclustered WHERE rid NOT IN (0 %s)"
+      "   AND NOT EXISTS(SELECT 1 FROM phantom WHERE rid=unclustered.rid)",
       blob_str(&deleteWhere)
     );
     blob_reset(&deleteWhere);
     if( nRow>0 ){
       md5sum_blob(&cluster, &cksum);