diff --git a/remotefilelog/__init__.py b/remotefilelog/__init__.py
--- a/remotefilelog/__init__.py
+++ b/remotefilelog/__init__.py
@@ -891,7 +891,9 @@
     ], _('hg debugkeepset'))
 def debugkeepset(ui, repo, **opts):
     # The command is used to measure keepset computation time
-    repackmod.keepset(repo)
+    def keyfn(fname, fnode):
+        return fileserverclient.getcachekey(repo.name, fname, hex(fnode))
+    repackmod.keepset(repo, keyfn)
     return
 
 @command('debugwaitonrepack', [
diff --git a/remotefilelog/repack.py b/remotefilelog/repack.py
--- a/remotefilelog/repack.py
+++ b/remotefilelog/repack.py
@@ -338,8 +338,16 @@
         processed.add(r)
 
         # populate keepkeys with keys from the current manifest
-        for filename, filenode in m.iteritems():
-            keepkeys.add(keyfn(filename, filenode))
+        if type(m) is dict:
+            # m is a result of diff of two manifests and is a dictionary that
+            # maps filename to ((newnode, newflag), (oldnode, oldflag)) tuple
+            for filename, diff in m.iteritems():
+                if diff[0][0] is not None:
+                    keepkeys.add(keyfn(filename, diff[0][0]))
+        else:
+            # m is a manifest object
+            for filename, filenode in m.iteritems():
+                keepkeys.add(keyfn(filename, filenode))
 
     return keepkeys