diff --git a/Annex/Init.hs b/Annex/Init.hs
index 4bd0955eaa..a552046a3a 100644
--- a/Annex/Init.hs
+++ b/Annex/Init.hs
@@ -37,7 +37,6 @@ import Annex.UUID
 import Annex.WorkTree
 import Annex.Fixup
 import Annex.Path
-import Annex.Concurrent
 import Config
 import Config.Files
 import Config.Smudge
@@ -134,8 +133,7 @@ initialize' mversion = checkInitializeAllowed $ do
 		then configureSmudgeFilter
 		else deconfigureSmudgeFilter
 	unlessM isBareRepo $ do
-		showSideActionAfter oneSecond "scanning for annexed files" $
-			scanAnnexedFiles
+		scanAnnexedFiles True
 		hookWrite postCheckoutHook
 		hookWrite postMergeHook
 	AdjustedBranch.checkAdjustedClone >>= \case
diff --git a/Annex/WorkTree.hs b/Annex/WorkTree.hs
index ac9c49b27d..33d9094872 100644
--- a/Annex/WorkTree.hs
+++ b/Annex/WorkTree.hs
@@ -15,6 +15,8 @@ import Annex.Content
 import Annex.ReplaceFile
 import Annex.CurrentBranch
 import Annex.InodeSentinal
+import Annex.Concurrent
+import Utility.ThreadScheduler
 import Utility.InodeCache
 import Git.FilePath
 import Git.CatFile
@@ -78,8 +80,8 @@ ifAnnexed file yes no = maybe no yes =<< lookupKey file
  - But if worktree file does not have a pointer file's content, it is left
  - as-is.
  -}
-scanAnnexedFiles :: Annex ()
-scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $ do
+scanAnnexedFiles :: Bool -> Annex ()
+scanAnnexedFiles initscan = showSideActionAfter oneSecond "scanning for annexed files" $ do
 	-- This gets the keys database populated with all annexed files,
 	-- by running Database.Keys.reconcileStaged.
 	Database.Keys.runWriter (const noop)
@@ -88,14 +90,19 @@ scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $ d
 	-- annex object file already exists, but its inode is not yet
 	-- cached and annex.thin is set. So, the rest of this makes
 	-- another pass over the tree to do that.
-	whenM (annexThin <$> Annex.getGitConfig) $ do
-		g <- Annex.gitRepo
-		(l, cleanup) <- inRepo $ Git.LsTree.lsTree
-			Git.LsTree.LsTreeRecursive
-			(Git.LsTree.LsTreeLong True)
-			Git.Ref.headRef
-		catObjectStreamLsTree l want g go
-		liftIO $ void cleanup
+	whenM
+		( pure initscan
+		<&&> annexThin <$> Annex.getGitConfig
+		<&&> inRepo Git.Ref.headExists
+		<&&> not <$> isBareRepo
+		) $ do
+			g <- Annex.gitRepo
+			(l, cleanup) <- inRepo $ Git.LsTree.lsTree
+				Git.LsTree.LsTreeRecursive
+				(Git.LsTree.LsTreeLong True)
+				Git.Ref.headRef
+			catObjectStreamLsTree l want g go
+			liftIO $ void cleanup
   where
 	-- Want to process symlinks, and regular files.
 	want i = case Git.Types.toTreeItemType (Git.LsTree.mode i) of
diff --git a/Command/Smudge.hs b/Command/Smudge.hs
index cbecd055f6..70fc9235ad 100644
--- a/Command/Smudge.hs
+++ b/Command/Smudge.hs
@@ -13,6 +13,7 @@ import Annex.Link
 import Annex.FileMatcher
 import Annex.Ingest
 import Annex.CatFile
+import Annex.WorkTree
 import Logs.Smudge
 import Logs.Location
 import qualified Database.Keys
@@ -262,6 +263,11 @@ getMoveRaceRecovery k file = void $ tryNonAsync $
 
 update :: CommandStart
 update = do
+	-- This gets run after a git checkout or merge, so it's a good
+	-- point to refresh the keys database for changes to annexed files.
+	-- Doing it explicitly here avoids a later pause in the middle of
+	-- some other action.
+	scanAnnexedFiles False
 	updateSmudged (Restage True)
 	stop
 
diff --git a/Upgrade/V5.hs b/Upgrade/V5.hs
index 2db92d57f9..22200b0c80 100644
--- a/Upgrade/V5.hs
+++ b/Upgrade/V5.hs
@@ -47,7 +47,7 @@ upgrade automatic = flip catchNonAsync onexception $ do
 		, do
 			checkGitVersionForIndirectUpgrade
 		)
-	scanAnnexedFiles
+	scanAnnexedFiles True
 	configureSmudgeFilter
 	-- Inode sentinal file was only used in direct mode and when
 	-- locking down files as they were added. In v6, it's used more
diff --git a/doc/todo/display_when_reconcileStaged_is_taking_a_long_time/comment_1_7efa1d29b475b445cea6fe44d402b275._comment b/doc/todo/display_when_reconcileStaged_is_taking_a_long_time/comment_1_7efa1d29b475b445cea6fe44d402b275._comment
new file mode 100644
index 0000000000..517e507dfe
--- /dev/null
+++ b/doc/todo/display_when_reconcileStaged_is_taking_a_long_time/comment_1_7efa1d29b475b445cea6fe44d402b275._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 1"""
+ date="2021-06-08T15:21:02Z"
+ content="""
+Made `git-annex smudge --update` run the scan, and so the post-checkout or
+post-merge hook will call it. 
+
+That avoids the scenario shown above. But adding a lot of files to the
+index can still cause a later pause for reconcileStaged without indication
+what it's doing.
+"""]]