I have a suggestion, but no idea how image boards in general or e621 in particular work. So I'm sorry, if this is a silly, impossible idea.
If someone posts a higher quality version of a pic(higher res or something), the lower quality one is usually deleted. But then comments, tags, favs etc. are deleted too. Is it possible to add a "Flag for Replacement" function? One could upload the higher quality version, then flag the old one for replacement, a mod looks into it and then merges favs, tags etc.
Or are you already doing this, if someone adds a higher-res version of a pic? Maybe it wouldn't need an extra function at all.
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