I'm again (or still?) observing some form of the original issue. After finding out the pattern, I'll come back again later to describe it.
Briefly described, the scenario is just like before. Inbox opened, the messages are being grabbed in chunks of 5 days. I've a conversation "Abcdef", consisting of say 80 messages, spanning 15 days. I'm reading them, swiping from the oldest towards the most recent ones. Sometimes I switch to another application, then come back to AquaMail. Sometimes I switch to another conversation, then return to continue reading the "Abcdef".
At some point I notice that I can't swipe further, or I can, but the thread has only e.g. 46 messages from the last 5 days. The older messages are gone. I definitely do not update the Inbox in between, or send any messages, or else, just read them.
I just have to spot the exact moment.
[edit] The only thing, which springs in my mind, is possibly a new messages appearing in the Inbox.
Sent from a touch display, which took care of perfectly scrambling my thoughts.