I've been using KDE/Kontact for a few years and I had managed to import and organize nearly 20 years of emails; all stored on an external encrypted drive.

Yesterday I upgraded to 15.10, and Kmail/Kontact/etc started crashing due to a "resource missing" error. No, my email was not open during the upgrade - nothing was running. I closed everything, kicked off the upgrade, and walked away.

I changed my local account to use /home/<user>/mail folder temporarily, which resolved the crashing.

When I pointed my local folder path back to my encrypted drive it doesn't crash anymore, but my 20 years of backed up email are now MISSING.

How do I recover them, or am I completely screwed?

Don't ask me why I "don't have a backup" - that's what the external drive was for. Kontact/Kmail/whatever had no business removing what was currently in place.

This is a pretty unusual setup, so I'm asking for information around.
Did you see if access times etc were changed on the drive? Were you using POP3 or IMAP?

Created and Modified times are both listed as 11/8/2015, which I believe was the day of the upgrade. Last accessed time is today.

IMAP, however that shouldn't have anything at all to do with the Local folders that were changed. It is/was set up in mbox format.

Ok, now it's clearer. So you were using mbox, and mails went missing. Please file a bug on bugs.kde.org with severity critical. I'll try to get someone to look at this.