This is a report only; I’ve resolved the issue manually.
I have two Linux laptops whose sync list includes a qmail-style Maildirs directory, under which are various dirs (Main, accts, mutt, …), each of which has the usual cur, new, and tmp dirs. The only special feature of this Maildirs/ directory is that my Androis phone does not sync it. The two laptops poll for mail every hour, one half hour apart, for unimportant reasons.
Last week, one of the laptops reported 3 files under Maildirs/Main/new which would not sync to the other laptop. I tried shutting down both syncthings and restarting them both at the same time. Tried shuttingdown each individually. Nothing would sync those three files. Subsequent mail fetches by both laptops brought in new emails in that same Maildirs/Main/new dir which did sync both ways, and reading email moved files from new to cur which synced, all the while those three files remained unsyncable.
I eventually gave up after several hours, created a tarball of those three files, the tarball synced, I untarred it on the other laptop, read those three emails which moved them to …/cur, which syncthing recognized and synced the change.
At this point, I wish I had documented every single step; I’m sure to have misremembered some details. But I didn’t, it’s all from memory, and I’ve seen nothing like it before or since. How those three files could remain unsynced while other files in the same dir synced around them over several hours … and then sync properly once I copied them manually and changed their parent dir … a mystery to me.