The short version is I'm starting on a large rebranding effort, part of which will involve re-exporting older work with new branding and higher resolution, as well as migrating a lot of content to different accounts.
So is there any option available other than uploading new versions and flagging the old ones? Yes, I could just leave them as is, but I'm going to be breaking a lot of source links so will be updating the e621 posts anyway, and would rather not add several dozen deleted posts to my account. Also, I assume dealing with the post that way is inconvenient.

you can ask an admin to get into the replacements beta, which allows you to replace the image in a post directly without having to create a whole new post

i got the permission myself from rainbow dash when i decided to replace all the old 720x1280 chikn nugget videos with higher bitrate 1080x1920 versions. it might not be the same as what you have in mind, but it's sure as hell faster than doing it traditionally and i can certainly help with your rebranding effort if you need it

If all else fails, you can ask the admins to manually increase your upload limit if too many of your posts get deleted. They usually acquiesce unless the reason your upload went negative was that you were uploading poor quality or forbidden content.