diff --git a/Logs/MetaData.hs b/Logs/MetaData.hs
index 4610ef481f..5527ea7604 100644
--- a/Logs/MetaData.hs
+++ b/Logs/MetaData.hs
@@ -96,7 +96,7 @@ getCurrentMetaData' getlogfile k = do
 	showts = formatPOSIXTime "%F@%H-%M-%S"
 
 getCurrentRemoteMetaData :: UUID -> Key -> Annex RemoteMetaData
-getCurrentRemoteMetaData u k = mkRemoteMetaData u <$>
+getCurrentRemoteMetaData u k = extractRemoteMetaData u <$>
 	getCurrentMetaData' remoteMetaDataLogFile k
 
 {- Adds in some metadata, which can override existing values, or unset
diff --git a/Remote/S3.hs b/Remote/S3.hs
index 29adb5643f..b39a2413d3 100644
--- a/Remote/S3.hs
+++ b/Remote/S3.hs
@@ -18,8 +18,9 @@ import qualified Aws.S3 as S3
 import qualified Data.Text as T
 import qualified Data.Text.Encoding as T
 import qualified Data.ByteString.Lazy as L
-import qualified Data.ByteString as S
+import qualified Data.ByteString as BS
 import qualified Data.Map as M
+import qualified Data.Set as S
 import Data.Char
 import Network.Socket (HostName)
 import Network.HTTP.Conduit (Manager)
@@ -44,8 +45,9 @@ import Remote.Helper.Export
 import qualified Remote.Helper.AWS as AWS
 import Creds
 import Annex.UUID
-import Logs.RemoteState
 import Logs.Web
+import Logs.MetaData
+import Types.MetaData
 import Utility.Metered
 import qualified Annex.Url as Url
 import Utility.DataUnits
@@ -256,7 +258,7 @@ storeHelper info h f object p = case partSize info of
  - that is difficult. -}
 retrieve :: Remote -> S3Info -> Maybe S3Handle -> Retriever
 retrieve r info (Just h) = fileRetriever $ \f k p -> do
-	loc <- getS3VersionID info (uuid r) k (T.pack $ bucketObject info k)
+	loc <- eitherS3VersionID info (uuid r) k (T.pack $ bucketObject info k)
 	retrieveHelper info h loc f p
 retrieve r info Nothing = case getpublicurl info of
 	Nothing -> \_ _ _ -> do
@@ -298,7 +300,7 @@ checkKey r info Nothing k = case getpublicurl info of
 			checkBoth (geturl $ bucketObject info k) (keySize k)
 checkKey r info (Just h) k = do
 	showChecking r
-	loc <- getS3VersionID info (uuid r) k (T.pack $ bucketObject info k)
+	loc <- eitherS3VersionID info (uuid r) k (T.pack $ bucketObject info k)
 	checkKeyHelper info h loc
 
 checkKeyHelper :: S3Info -> S3Handle -> (Either S3.Object S3VersionID) -> Annex Bool
@@ -717,7 +719,7 @@ debugMapper level t = forward "S3" (T.unpack t)
 s3Info :: RemoteConfig -> S3Info -> [(String, String)]
 s3Info c info = catMaybes
 	[ Just ("bucket", fromMaybe "unknown" (getBucketName c))
-	, Just ("endpoint", w82s (S.unpack (S3.s3Endpoint s3c)))
+	, Just ("endpoint", w82s (BS.unpack (S3.s3Endpoint s3c)))
 	, Just ("port", show (S3.s3Port s3c))
 	, Just ("storage class", showstorageclass (getStorageClass c))
 	, if configIA c
@@ -773,12 +775,27 @@ setS3VersionID info u k vid
 	| otherwise = noop
 
 setS3VersionID' :: UUID -> Key -> S3VersionID -> Annex ()
-setS3VersionID' u k vid = setRemoteState u k (formatS3VersionID vid)
+setS3VersionID' u k vid = addRemoteMetaData k $
+	RemoteMetaData u (updateMetaData s3VersionField v emptyMetaData)
+  where
+	v = mkMetaValue (CurrentlySet True) (formatS3VersionID vid)
 
-getS3VersionID :: S3Info -> UUID -> Key -> S3.Object -> Annex (Either S3.Object S3VersionID)
-getS3VersionID info u k fallback
-	| versioning info = maybe (Left fallback) Right <$> getS3VersionID' u k
+getS3VersionID :: UUID -> Key -> Annex [S3VersionID]
+getS3VersionID u k = do
+	(RemoteMetaData _ m) <- getCurrentRemoteMetaData u k
+	return $ mapMaybe parseS3VersionID $ map unwrap $ S.toList $
+		metaDataValues s3VersionField m
+  where
+	unwrap (MetaValue _ v) = v
+
+s3VersionField :: MetaField
+s3VersionField = mkMetaFieldUnchecked "V"
+
+eitherS3VersionID :: S3Info -> UUID -> Key -> S3.Object -> Annex (Either S3.Object S3VersionID)
+eitherS3VersionID info u k fallback
+	| versioning info = getS3VersionID u k >>= return . \case
+		[] -> Left fallback
+		-- It's possible for a key to be stored multiple timees in
+		-- a bucket with different version IDs; only use one of them.
+		(v:_) -> Right v
 	| otherwise = return (Left fallback)
-
-getS3VersionID' :: UUID -> Key -> Annex (Maybe S3VersionID)
-getS3VersionID' u k = maybe Nothing parseS3VersionID <$> getRemoteState u k
diff --git a/Types/MetaData.hs b/Types/MetaData.hs
index f0dd833d6d..d4fee39ca1 100644
--- a/Types/MetaData.hs
+++ b/Types/MetaData.hs
@@ -37,7 +37,7 @@ module Types.MetaData (
 	ModMeta(..),
 	modMeta,
 	RemoteMetaData(..),
-	mkRemoteMetaData,
+	extractRemoteMetaData,
 	fromRemoteMetaData,
 	prop_metadata_sane,
 	prop_metadata_serialize
@@ -291,8 +291,8 @@ data RemoteMetaData = RemoteMetaData UUID MetaData
 
 {- Extracts only the fields prefixed with "uuid:", which belong to that
  - remote. -}
-mkRemoteMetaData :: UUID -> MetaData -> RemoteMetaData
-mkRemoteMetaData u (MetaData m) = RemoteMetaData u $ MetaData $
+extractRemoteMetaData :: UUID -> MetaData -> RemoteMetaData
+extractRemoteMetaData u (MetaData m) = RemoteMetaData u $ MetaData $
 	M.mapKeys removeprefix $ M.filterWithKey belongsremote m
   where
 	belongsremote (MetaField f) _v = prefix `isPrefixOf` CI.original f
diff --git a/doc/todo/versioning_in_export_remotes.mdwn b/doc/todo/versioning_in_export_remotes.mdwn
index 34adaf1efe..e48bf1768c 100644
--- a/doc/todo/versioning_in_export_remotes.mdwn
+++ b/doc/todo/versioning_in_export_remotes.mdwn
@@ -82,7 +82,3 @@ keys that are not used in the current export doesn't help because another
 repository may have changed the exported tree and be relying on the dropped
 key being present in the export. Unless... Could export conflict resultion
 somehow detect that?
-
-Another reason DELETE from appendonly is not supported is that only one
-version ID is stored per key, but the same key could have its content in
-the bucket multiple times under different version IDs.