I have no idea what deleting MSF files would do to help as they are index files for your already downloaded stored mail. You do not say anything about the index being corrupt. So I will ignore it.

The popstate.dat file however does contain the status of the downloads from the server. If anything corrupts the file, prevents it being written or chops off the connection before it can be written then what you see occurs. So for future prevention you should exclude that file from anti virus scanning, and probably you also need to disable your anti virus from scanning mail, as the chopping of the connection is the probable cause and it would be the culprit.

This addon will help in getting rid of duplicates.

https://addons.mozilla.org/en-US/thunderbird/addon/remove-duplicate-messages/?src=ss or https://addons.mozilla.org/en-US/thunderbird/addon/remove-duplicate-messages-alte/?src=search

Thank you very much for taking the time to respond. Deleteing .msf files was suggested consistently on other knowledge base posts.

I manually deleted all the duplicates before your solution was posted, but I've noted the addon for the future and have excluded the popstate.dat file from scanning.

Hopefully the issue won't recur and I'll post again if it does.

Again, thank you for your time and clarification!