IRS Refund delays - Paper filing

Last Monday I found a new notice on the IRS web site. Specifically, under the section entitled What You Can Expect / Filed a Tax Return.

It looks like they're finally acknowledging they've totally lost some paper forms:

If you are due a refund, filed on paper more than six months ago, and Where’s My Refund? does not have any information about the status of your return, you should resubmit your tax return, electronically if possible.
I re-filed my return on their FreeFile site. It was accepted this time and my refund was deposited to my account on Thursday.

Oddly enough, it was for a little more than I was expecting. Presumably, they added interest since my initial paper filing in February. So they knew I'd filed my paper return all along, even though their "where's my refund" web site claimed otherwise.

To add to the mystery, this time when I re-submitted my FreeFile return, the exact same one they kept rejecting in February, it identified a different error than they'd shown in February. This time they were correct; I had made a one-digit error in an ID number on a 1099. I fixed that and it was accepted right away.

Originally it had shown an error in my bank account number, which of course I'd checked and re-checked numerous times, and it was correct, then and now.
 
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