In T423823, we were asked to delete a file that had nearly 5k versions uploaded. Since the limit defined by FileOpBatch is just 1000, the following error message appeared:
Unlike big pages, nothing like bigdelete or DeleteRevisionsBatchSize exists, making the deletion tricky to carry out. I ended up using an ad hoc JS to delete most versions individually (just to get it under 1000), and then regular MediaWiki deletion feature worked as expected.
However, there really should be either some sort of batching (similar to DeleteRevisionsBatchSize), or there should be an upper limit on the number of versions one file can have.
See also: T198176: Mediawiki page deletions should happen in batches of revisions. See also T425897: Future of filearchive table for potential long-term solution.
