When on an adjusted branch, git annex sync will sync the submodule commit for the initial addition of a submodule, but it doesn't seem to sync changes in the recorded commit. Here's a demo of the issue based off of Michael's script at DataLad's issue 4292.

cd "$(mktemp -d --tmpdir gx-sync-demo-XXXXXXX)"

git init
git annex init
git commit --allow-empty -mc0
git annex adjust --unlock

git init sub
git -C sub commit --allow-empty -mc0
git submodule add ./sub
git commit -m'add sub'
# A new submodule is sync'd.
git annex sync --no-commit --no-push --no-pull --no-content

git -C sub commit --allow-empty -mc1
git add sub
git commit -m'sub update'

# A change in the submodule ID is not.
git annex sync --no-commit --no-push --no-pull --no-content
git diff master..

With a git-annex built from 8.20200309-62-gc8fec6ab0, the submodule remains modified between master and adjusted/master(unlocked)).

diff --git a/sub b/sub
index ed67764..a27fd83 160000
--- a/sub
+++ b/sub
@@ -1 +1 @@
-Subproject commit ed6776462d0842bf0a317d2e3ee1983572a217ff
+Subproject commit a27fd837958466ba4fb751a3de139c03548be1ad

I was able to resolve the issue (i.e. the above demo outputs an empty diff) with the patch below, though that might of course be the completely wrong way to fix this.

Thanks in advance for looking into this issue.

From fa3a4be5497300b9b39e121008b474e9dd405fd3 Mon Sep 17 00:00:00 2001
From: Kyle Meyer <kyle@kyleam.com>
Date: Tue, 17 Mar 2020 22:16:06 -0400
Subject: [PATCH] adjust: Propagate submodule changes back to original branch

When the recorded submodule commit changes on an adjusted branch, the
change is carried in the function that reverseAdjustedCommit passes
for adjustTree's adjusttreeitem parameter.  Update the CommitObject
handling in adjustTree to consider adjusttreeitem so that a submodule
change is synced back.
 Git/Tree.hs | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/Git/Tree.hs b/Git/Tree.hs
index da05a3fa5..9627ae969 100644
--- a/Git/Tree.hs
+++ b/Git/Tree.hs
@@ -237,8 +237,12 @@ adjustTree adjusttreeitem addtreeitems resolveaddconflict removefiles r repo =
                let !modified' = modified || slmodified || wasmodified
                go h modified' (subtree : c) depth intree is'
            Just CommitObject -> do
-              let ti = TreeCommit (LsTree.file i) (LsTree.mode i) (LsTree.sha i)
-              go h wasmodified (ti:c) depth intree is
+              let ti = TreeItem (LsTree.file i) (LsTree.mode i) (LsTree.sha i)
+              v <- adjusttreeitem ti
+              let commit = tc $ fromMaybe ti v
+              go h wasmodified (commit:c) depth intree is
+              where
+                  tc (TreeItem f m s) = TreeCommit f m s
            _ -> error ("unexpected object type \"" ++ decodeBS (LsTree.typeobj i) ++ "\"")
        | otherwise = return (c, wasmodified, i:is)

applied, thanks! --Joey