I just came across this thread. I had the same problem over and over again, every few months. I switched to IMAP from POP3, but it still happened. Here is a link to the thread–it’s old now, from 2017.
https://forum.emclient.com/t/suddenly-downloaded-all-of-my-old-emails-again/43522
Not sure if this will help, but at least you know you are not the only one with the problem.