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I think I've solved my issue here, but thought it might be worth adding to the documentation.
I had a file I wanted to remove from the history, which has been around for a few months, and so now made it into several branches. However, I didn't want to rewrite more than necessary, and some early commits had GPG signatures, which I've worked out you can't handle.
The approach I found, which seems to have worked, is
git filter-repo --refs $(git for-each-ref --contains first-commit-sha-with-problematic-file --format "%(refname)" )
(Together with the arguments to specify the file I wanted removed).
It wasn't clear from the documentation that --refs would accept a list like this.
If there's a better way to do this, I'd also love to know (and also worth adding to the documentation).
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