OK.
Did the messages returned in the morning (the app does some trimming / cleaning of what it stores at 3am)
Or did they return after some (later in the day) mail check?
I'm going to try and reproduce this with one of my accounts, please confirm your settings:
- Account is POP3
- Messages to sync at 100
- Messages to cache at 250 (both account level settings)
- You receive how many messages a day, approximately? A few, a dozen, a few dozsen?
- As a rule, you hide most of them in the app?
- Finally, long press the account -> options and folders -> account options -> is "remove deleted messages" turned on or off?