I have a repo for which git annex fsck --all goes through without any complaints, and git fsck produces

Checking object directories: 100% (256/256), done.
error in tree 97abf6de76c0c56593f78d2f55b4c60d04345281: gitmodulesSymlink: .gitmodules is a symbolic link
Checking objects: 100% (998477/998477), done.
Checking connectivity: 998477, done.
dangling tree f9a2b542f57770c135631de1ae590475fc0caa54

but running git annex repair --force,

repair Running git fsck ...
Unpacking all pack files.
Unpacking objects: 100% (998477/998477), 64.95 MiB | 359.00 KiB/s, done.
Initialized empty Git repository in /tmp/tmprepoqPmkhi/.git/
Trying to recover missing objects from remote A.
fatal: '[a path I censored]' does not appear to be a git repository
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Trying to recover missing objects from remote B.
Unpacking all pack files.
Unpacking objects: 100% (923941/923941), 63.54 MiB | 367.00 KiB/s, done.
[A couple of other cases of remotes not available.]
git-annex: repair: 1 failed

Is the failure likely related to the gitmodulesSymlink error? If so, what could I do about it? If not, how do I figure out what's going on?

Regarding the .gitmodules complaint: The repo has a subfolder with its own .git and .gitmodules, and although nothing in there is commited into the main repo now, I did in the past accidentally, temporarily commit the subfolder/.gitmodules into the main repo.

I don't actually find anything wrong with the repo, the only reason I'm running repair on it is because a remote of it is missing some files, although it claims to be all synced up.

This is on version 8.20200226. I would be happy to try on a more recent one, if there's a way to do so on Ubuntu without compiling from source.