refreshImageMetadata.php maintenance script should handle oldimage.oi_metadata and filearchive.fa_metadata (in addition to image.img_metadata).
I have looked into this today and it looks a lot worse than it seemed. We really have very different handling for current revision, old revisions and deleted revisions of files. It would be easy enough to just triplicate everything, but that would be horrible for future maintenance; and I don't really know enough about our upload backend code to come up with a sensible way of sharing this functionality.
So I'm throwing the towel and hereby deciding that this is not so important. We never display the metadata for old or deleted revisions, so for MediaWiki, it's enough to make sure they are updated when a file is undeleted or reverted. I'm doing this in https://gerrit.wikimedia.org/r/302973, and if anyone ever wants to analyze metadata for historical revisions, well, they'll have to sort it out themselves.