lost POP3 Mail after El Capitan installed

Following the upgrade from Yosemite to El Capitan, I discovered that my POP3 Mail Inbox and Outbox were both empty. (I also have IMAP mail accounts and those mail messages are on the providers' servers.)

Note that I've got my POP3 account configured such that mail is left on their server for 30 days even after it is downloaded to my iMac, so the messages are still available if I log in to that account via their web interface.

I tried deleting the POP3 account in OS X Mail and then re-creating it, but to no avail.

I don't recall this ever happening with any other OS X upgrade.

Has anyone else experienced this?

Also, Apple has virtually gutted the Mail Activity window, which was a useful monitor of how the various messages from all my accounts were received and sent. And I was able to leave the Activity window open in the background behind the Mail app itself. Now no more to both of these features. The Activity window merely shows something is either coming in or going out, but not by account. The Activity window cannot be placed in the background but stays in the foreground unless closed. Not happy with this.