If you are using POP3 (with all devices set to leave a copy on the server) rather than IMAP there is a potential for this. I've not seen it happen before as you described where 2 devices were afflicted this way at the same time. I have seen a case where a windows computer infected with malware orphaned off a mail file when it became corrupt, causing all the mail on the server to be downloaded again.
If POP3 is your choice you should consider switching to IMAP. POP3 is yesterday's technology.
IMAP maintains server side mail folders that can be synched with local folders on multiple devices. This is a much better approach than using POP which can only be configured to leave an inbox copy on the server. The added functionality provided by IMAP means that you don't have to filter thru the same messages on multiple devices, as you read messages on one device they will change from read to unread on the other device as well, when the message is moved or deleted on one device it is on the other was well. Additionally webmail remains synched as well.