diff --git a/Annex/Ssh.hs b/Annex/Ssh.hs
index 8304e04c1a..e7c2114b6f 100644
--- a/Annex/Ssh.hs
+++ b/Annex/Ssh.hs
@@ -154,8 +154,11 @@ sshConnectionCachingParams socketfile =
 sshSocketDirEnv :: String
 sshSocketDirEnv = "GIT_ANNEX_SSH_SOCKET_DIR"
 
-{- ssh connection caching creates sockets, so will not work on a
- - crippled filesystem. -}
+{- Returns the directory where ssh connection caching sockets can be
+ - stored.
+ - 
+ - The directory will be created if it does not exist.
+ -}
 sshCacheDir :: Annex (Maybe FilePath)
 sshCacheDir = eitherToMaybe <$> sshCacheDir'
 
@@ -169,7 +172,10 @@ sshCacheDir' =
 				Just tmpdir -> 
 					liftIO $ catchMsgIO $
 						usetmpdir tmpdir
-			, Right <$> fromRepo gitAnnexSshDir 
+			, do
+				d <- fromRepo gitAnnexSshDir
+				createAnnexDirectory d
+				return (Right d)
 			)
 		, return (Left "annex.sshcaching is not set to true")
 		)
@@ -221,7 +227,6 @@ prepSocket socketfile sshhost sshparams = do
 	-- Cleanup at shutdown.
 	Annex.addCleanup SshCachingCleanup sshCleanup
 	
-	liftIO $ createDirectoryIfMissing True $ parentDir socketfile
 	let socketlock = socket2lock socketfile
 
 	Annex.getState Annex.concurrency >>= \case
diff --git a/Assistant/Threads/Merger.hs b/Assistant/Threads/Merger.hs
index 82802fbb29..ac9435122a 100644
--- a/Assistant/Threads/Merger.hs
+++ b/Assistant/Threads/Merger.hs
@@ -26,8 +26,9 @@ import qualified Command.Sync
 mergeThread :: NamedThread
 mergeThread = namedThread "Merger" $ do
 	g <- liftAnnex gitRepo
-	let dir = fromRawFilePath (Git.localGitDir g) </> "refs"
-	liftIO $ createDirectoryIfMissing True dir
+	let gitd = fromRawFilePath (Git.localGitDir g)
+	let dir = gitd </> "refs"
+	liftIO $ createDirectoryUnder gitd dir
 	let hook a = Just <$> asIO2 (runHandler a)
 	changehook <- hook onChange
 	errhook <- hook onErr
diff --git a/Assistant/Threads/TransferWatcher.hs b/Assistant/Threads/TransferWatcher.hs
index 181cb10f55..e4316ffcd2 100644
--- a/Assistant/Threads/TransferWatcher.hs
+++ b/Assistant/Threads/TransferWatcher.hs
@@ -15,6 +15,7 @@ import Logs.Transfer
 import Utility.DirWatcher
 import Utility.DirWatcher.Types
 import qualified Remote
+import Annex.Perms
 
 import Control.Concurrent
 import qualified Data.Map as M
@@ -24,7 +25,7 @@ import qualified Data.Map as M
 transferWatcherThread :: NamedThread
 transferWatcherThread = namedThread "TransferWatcher" $ do
 	dir <- liftAnnex $ gitAnnexTransferDir <$> gitRepo
-	liftIO $ createDirectoryIfMissing True dir
+	liftAnnex $ createAnnexDirectory dir
 	let hook a = Just <$> asIO2 (runHandler a)
 	addhook <- hook onAdd
 	delhook <- hook onDel
diff --git a/Assistant/WebApp/Configurators/Edit.hs b/Assistant/WebApp/Configurators/Edit.hs
index 59d8d61247..c82fbe248f 100644
--- a/Assistant/WebApp/Configurators/Edit.hs
+++ b/Assistant/WebApp/Configurators/Edit.hs
@@ -41,6 +41,7 @@ import Remote.Helper.Encryptable (extractCipher, parseEncryptionConfig)
 import Types.Crypto
 import Utility.Gpg
 import Annex.UUID
+import Annex.Perms
 import Assistant.Ssh
 import Config
 import Config.GitConfig
@@ -246,9 +247,9 @@ checkAssociatedDirectory cfg (Just r) = do
 	repoconfig <- M.lookup (Remote.uuid r) <$> readRemoteLog
 	case repoGroup cfg of
 		RepoGroupStandard gr -> case associatedDirectory repoconfig gr of
-			Just d -> inRepo $ \g ->
-				createDirectoryIfMissing True $
-					fromRawFilePath (Git.repoPath g) </> d
+			Just d -> do
+				top <- fromRawFilePath <$> fromRepo Git.repoPath
+				createWorkTreeDirectory (top </> d)
 			Nothing -> noop
 		_ -> noop
 
diff --git a/CHANGELOG b/CHANGELOG
index b7b81c227a..cd41f23c8f 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,5 +1,8 @@
 git-annex (8.20200227) UNRELEASED; urgency=medium
 
+  * Improve behavior when a directory git-annex is writing to gets
+    unmounted. Previously it could in some cases re-create the mount point
+    and directory tree, and even write object contents to the wrong disk.
   * Bugfix: Don't ignore --debug when it is followed by -c.
   * whereis: If a remote fails to report on urls where a key
     is located, display a warning, rather than giving up and not displaying
diff --git a/doc/todo/stop_using_createDirectoryIfMissing_True.mdwn b/doc/todo/stop_using_createDirectoryIfMissing_True.mdwn
index 3faca053f3..f82555a47d 100644
--- a/doc/todo/stop_using_createDirectoryIfMissing_True.mdwn
+++ b/doc/todo/stop_using_createDirectoryIfMissing_True.mdwn
@@ -28,3 +28,5 @@ point, which can be either .git/annex or the top of the worktree depending
 on what's being done. --[[Joey]]
 
 [[!tag confirmed]]
+
+> [[fixed|done]], all relevant calls have been converted. --[[Joey]]