As an update, I've performed a factory reset on my device and re-added the books I had previously. It works as expected now, new annotations are saved. I still don't have any idea why it happened in the first place and what I should avoid to make it happen again in the future.
To me it seems clear that there is a need for better annotations functionality on reading devices. People have said so on this and other threads and the
Annotations plugin thread is constantly busy with questions, ideas and development. There is a big itch there that needs to be scratched.
How do people here feel it would be the best way to express this need towards Kobo? I might have my own ideas as to what I'd like to see on my Forma, but my own, isolated ideas don't matter much. I'd like to come up with a way to express this towards Kobo in a way that will be taken into account. Maybe something like a petition by the MobileRead Forums? Express the general need and leave it to Kobo for the implementation.