A while back, I switched from Ulysses to iA Writer (via Bear Writer as it happens, but that's not particularly pertinent) for my writing needs.
I had given Ulysses a pretty good review but hit upon some iCloud synching problems with it. The problem presented itself to me via Ulysses, but it was actually part of a generic iCloud syncing problem.
I got Apple Support involved but no solution was found at the time. It did eventually clear after a few maintenance releases of iOS and macOS, but by that time I'd ditched Ulysses because of this problem.
By chance, I recently came upon a very similar Ulysses synching problem as detailed by Bryce Wray. I wish that post had been around when I had my problem. I could not otherwise find much of use to refer to back in 2018. It details quite nicely how so-called shoebox apps sometimes have a problem syncing via iCloud.
I’m a little puzzled by how Bryce actually cured the problem — albeit a problem with iCloud rather than Ulysses — such that he can trust Ulysses again. He doesn’t mention that. [update - see addendum]
Nevertheless, his post remains a good source of information about why this problem occurs. I wanted to log it here because I recently exchanged a few emails with someone who contacted me about this very problem, having seen my own posts on the issue.
It's not that I plan to move back to Ulysses myself. iA Writer suits my workflow much better at the moment and, besides, it's an excellent markdown writing app in itself.
Addendum: 17 July 2020
After exchanging a few very pleasant emails with Bryce, he kindly cleared up the issue of how Ulysses regained his trust. You can read it in the yellow box towards the end of his Boxed In post, which I referenced above.