Bitbucket can not create merge diff or merge Edited

We're using the Gitflow Workflow and have migrated from a Mercurial repo (where we were using the same workflow).

Between the previous release and this, we did some management of a third-party library, previously cloned from git (when we were using Mercurial). Not entirely sure about this part, but I believe as part of the conversion, the .git-folder in the library was deleted.

Now, I created a pull request to merge our release branch (which does not have the .git folder) with the master branch (which has the .git folder). Bitbucket Server says "Bitbucket Server could not create the merge diff for this pull request"

The merge button is available, and if I try to perform a merge I get

'/usr/bin/git reset --quiet 4d5ac1b2a903ab1cd371c2fb39dc87fca107fdfa --' exited with code 128 saying: error: Invalid path 'vendor/CException/.git/HEAD' fatal: make_cache_entry failed for path 'vendor/CException/.git/HEAD'

I can however merge locally on my machine.

Any ideas on how to resolve this?

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