Here's what I would do. Once you have downloaded all the messages in POP Peeper:
1) Exit POP Peeper and make a backup of the data.db file for that account
2) Edit the account and disable it and I would probably change the server address to something that would fail (to prevent myself from accidentally trying to check it; note that if they delete your account, PP won't be able to access it and this would not trigger PP to remove the messages, but if they were to delete your messages before deleting your account, then PP may login successfully, see there's no messages and then remove them from its list); you can disable the "remove messages not on server" option on the Edit/Advanced page for some extra insurance
3) If you have POP Peeper Pro v5 (available in the beta now, or the official release later), you can archive the messages in the account (right-click on the account and select "archive messages") and then upload the archived messages to a different account (ie. I would recommend putting them into a separate folder of that account). This way you'll have a "cloud" backup of your messages and not just local files. Note that you can archive them now whether you have Pro-v5 or not, it's the uploading that will require Pro-v5.
POP Peeper: Tech support, suggestions, discussion, etc.
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