After filing an Outlook email into any folder, it disappears. Any idea why (or where it went)?

Answer 1

Most likely you have auto-archiving turned on and Outlook has archived your old e-mails to its Archived Items folder. Open that folder and you will find all of the archived mail items.

Answer 2

Check the "view" for that folder. I once turned on the view, show all unread, and forgot. lost all my e mails for a little while.
also check your archive.
also check your rules for that folder, you may have a rule to move that e mail to another folder.
to find it quickly, just search for that sender.