diff --git a/Annex/Branch.hs b/Annex/Branch.hs
index a653a49955..b2b1ed3e40 100644
--- a/Annex/Branch.hs
+++ b/Annex/Branch.hs
@@ -268,7 +268,7 @@ withIndex' :: Bool -> Annex a -> Annex a
 withIndex' bootstrapping a = do
 	f <- fromRepo gitAnnexIndex
 	bracketIO (Git.Index.override f) id $ do
-		unlessM (liftIO $ doesFileExist f) $ do
+		checkIndexOnce $ unlessM (liftIO $ doesFileExist f) $ do
 			unless bootstrapping create
 			liftIO $ createDirectoryIfMissing True $ takeDirectory f
 			unless bootstrapping $ inRepo genIndex
diff --git a/Annex/BranchState.hs b/Annex/BranchState.hs
index 0950e9a967..977c4aa107 100644
--- a/Annex/BranchState.hs
+++ b/Annex/BranchState.hs
@@ -37,6 +37,14 @@ invalidateCache = do
 	state <- getState
 	setState state { cachedFile = Nothing, cachedContent = "" }
 
+{- Runs an action to check that the index file exists, if it's not been
+ - checked before in this run of git-annex. -}
+checkIndexOnce :: Annex () -> Annex ()
+checkIndexOnce a = unlessM (indexChecked <$> getState) $ do
+	a
+	state <- getState
+	setState state { indexChecked = True }
+
 {- Runs an action to update the branch, if it's not been updated before
  - in this run of git-annex. -}
 runUpdateOnce :: Annex () -> Annex ()
@@ -48,9 +56,6 @@ runUpdateOnce a = unlessM (branchUpdated <$> getState) $ do
  - is known to have not changed, or git-annex won't be relying on info
  - from it. -}
 disableUpdate :: Annex ()
-disableUpdate = Annex.changeState setupdated
-	where
-		setupdated s = s { Annex.branchstate = new }
-			where
-				new = old { branchUpdated = True }
-				old = Annex.branchstate s
+disableUpdate = do
+	state <- getState
+	setState state { branchUpdated = True }
diff --git a/Types/BranchState.hs b/Types/BranchState.hs
index 777edb32cb..e5b2291f3b 100644
--- a/Types/BranchState.hs
+++ b/Types/BranchState.hs
@@ -9,6 +9,7 @@ module Types.BranchState where
 
 data BranchState = BranchState {
 	branchUpdated :: Bool, -- has the branch been updated this run?
+	indexChecked :: Bool, -- has the index file been checked to exist?
 
 	-- the content of one file is cached
 	cachedFile :: Maybe FilePath,
@@ -16,4 +17,4 @@ data BranchState = BranchState {
 }
 
 startBranchState :: BranchState
-startBranchState = BranchState False Nothing ""
+startBranchState = BranchState False False Nothing ""