Kostya,
Yes, that's the first thing I did (setting the messages to sync to 1000) but they didn't appear after many forced syncs.
To summarize:
1. I had some messages I sent to some people (a couple from January and some more from last December).
2. They were initially stored at Sent items.
3. I then moved them to another folder (a label on Gmail) through my Postbox desktop client where I store both received and sent messages.
4. A couple of days later I wanted to check those messages while on the road with AquaMail and I couldn't find them.
5. There were just three messages more recent than those on that folder so it was easy to confirm they weren't there.
6. When again at home I checked that the messages were both at Gmail web and Postbox desktop client.
That's basically the issue. Why it happens... don't ask me.

I just copied all folders to another IMAP account on another provider I have and it works as expected. In my opinion something wrong should be happening with Gmail IMAP implementation that some software is handling it and some not.
I still don't see some messages (not the first two because I moved between folders and they appeared, as Paris Geek recommended).
Do you want me to delete the older 300 ones so I keep 215 only and see what happens?
Paris Geek,
Yes, I had sync at 250 before and when I saw those messages missing I changed it to 1000 (and cached to 10000). Anyway, after many sync tries they didn't appear. I even removed the folder and added it again but didn't work.
I do see the usefulness of this scenario to see if the logic can be improved in AquaMail. I only want the best for it (I know it's a lot of work and you should take it easy Kostya).
It seems I'm magnet for weird issues. :-(