Hi @JsPhoto, welcome to the forum!
This sounds like something I ran into a while ago (Repeated "Delete operation failed" due to file not found). In my case, I a database REPAIR (not recreate) was all that was needed.
That should also resolve your “missing files” error messages.
Sorry if I missed it in your post, but were you able to “manually” verify that the reported missing files were ACTUALLY no longer on the NextCloud destination?
If it’s still in your logs, try going back a bit further and see if you can find a log entry requesting the deletion of the now-reported-missing files. I believe that’s what happened to me - they were requested to be deleted, they WERE deleted, but then they were requested to be deleted again which started throwing the warnings.
I should note that --no-backend-verification is a good TESTING tool, but not really a good long term solution.