Maybe try this but I can't guarantee it's going to work.
I would also recommend making a backup of your AquaMail before starting.
First, I would make sure those folders are deleted with another email client besides just AquaMail.
Second, delete the account from AquaMail.
Third, Go into settings - Data Storage - Compact the Database (WARNING: this will delete old data from AquaMail).
Fourth, force close the app and clear cache (WARNING: don't clear app data as that will clear out everything from AquaMail).
Fifth, re-add the email account to AquaMail and what happens after that?