I believe the error is finally fixed. It's still quite difficult to pinpoint the cause. Clearing '''.msf''' files and compacting mailbox didn't make a difference although in some situations it may help. After removing account, deleting all relevant profile folders and files, re-adding the account, switching between "'''Move to this folder'''" and "'''Just mark as deleted'''" in "'''Server settings'''->'''When I delete a message'''" couple of times, applying '''download message limit''', restarting and removing the limit did the job. On a side note, inbox and other folders were not synchronised correctly to begin with. Weird, the problem was related only to one of many other accounts Thunderbird is connected to. Looks like a minor bug although for now problem seems to be gone.