Yes, I keep getting emails about how "AquaMail stopped working with my Yahoo account".... Not many, but a few a day.
One thing that *might* help is using Yahoo web mail (web site) to mark all your messages as "read", if you have a lot of them (say, hundreds).
Other than that, feel free to capture the issue in the app's debug log (see my signature below).
But I'm afraid that those *server side* issues are still for Yahoo to fix. I can only help identify them.
PS - I can now see that the original message is about Yahoo, but it's from 2013, and @schuttwm is not using Yahoo.
@schuttwm - only a debug log can help me see what's going on.
Please put the message back where it's causing trouble again, enable debug logging in AquaMail, including "raw session data", and capture the issue there.
See my signature, below, for more info about logging.