Since you have POP accounts, this is a major issue, and without that file nothing would prevent Mail from continuing to download all messages on the server!
What was the first version of OSX you were using when you established these accounts? In the Mail folder, please report all the files found at its root level? In the POP account folders, is there any file with MessageUids in it name?
I think you will need to purge the com.apple.mail.plist file, and once again setup your email accounts, but we should not this until we consider everything in the Mail folder itself.
Ernie