I have replied to your email with a more detailed response in regards to your file, but in case anyone else has this issue, as Ulysses can’t have sheets/documents nested within others (only within groups/folders), then if you have your sync settings set up where this will occur, the sync won’t work and will continue to say something needs syncing, even if you click “Sync Now”.
I’ve found a bit of a work around in that if I make the sheets in Ulysses it syncs it. However, I noticed that it changes the order of the sheets when they are nested together.
I sorta wished that if the items are nested together, they should remain manually sorted in order (the parent followed by children) so this could be a viable workaround to this dilemma