I deleted the repo, but not the vault, then cloned the repo & synced it with the obsidian folder again. Still had issues with that one Cyrillic file, but I reverted its deletion in WorkingCopy and it seems that things are all ok now.
edit:
I see that the new release of Working Copy says that it ‘fixes problems with Folder Sync when filenames contained diacritics.’
Seems quite likely that the folder sync issue I had may have been to do with that, still not entirely sure how much that had to with my other more serious problem, but it’s all been working fine after the first bit of faffing.