I am having the exact same problem. After migrating to a new iPad from a backup, I am able to access maybe 20% of the notes, with no particular pattern that I can find. When I try to access the others (I can see the notes “icon” but not it’s content), I get an error message that says that I will have access when the Penultimate finishes syncing, but that never happens.
I tried deleting and reinstalling the app, but that did not work.
Has anyone had any better luck?