Yes, there are “local” time signatures in this project, but I used them intentionally and would prefer to be able to still use them as that functionality is often very useful for me, whether for displaying independent time signatures or formatting barlines independently.
This particular flow does not require that functionality, so I deleted all time sigs in the flow (cmd+A, Edit > Filter > Time Signatures, delete) but as I try to reenter them in the normal manner (shift+M) the top staff does not want to recognize a time signature at the very beginning of the music (previously 3/8 with an 8th pickup). Putting a time signature after the first 8th note seems to be fine. The “displacement” bug still occurs at the same point in the music, as in my previous screenshot.
It seems I’ll have to put this all into a fresh flow, but I would hope to avoid having to do that for a larger project in the future!