Before I get around to that, I should inform you that the latest update (version 1.4a) has a bug-fix that fixes incorrect flip updates that were introduced in version 1.4, as mentioned in the relevant devlog. In hindsight, I think I should have more explicitly informed you of that.
Re-added some accidentally removed lines of code that updated the current flip state in PaperSkeleton, which likely would've introduced problems for PaperBoneAttachment3D's flipping logic if gone unchecked.
Did you update to 1.4a? If not, can you download it and use it to see if the update already fixes your problem? Just making sure, as itch.io's statistic tell me that no one has downloaded it thus far, though I don't know how frequently that counter updates.
Also, sorry for not responding too quickly. For some reason, itch.io's notifications seem to lag behind a bit for me, only popping up hours later.