Do I have to file for an extension now that I missed the deadline? How do I file one?

If you're expecting a refund, you're actually in good shape! The deadline to file is technically only a firm deadline if you *owe* taxes. When you're due a refund, there's no penalty for filing late. That said, the IRS generally gives you up to 3 years from the original filing deadline to claim your refund. After that, your refund money becomes property of the U.S. Treasury. So while you don't need to worry about penalties right now, you definitely want to make sure your return gets processed. Since you already mailed in your return with an explanation letter, the best thing to do now is just wait. The IRS is currently taking about 6-8 weeks to process paper returns. Make sure you kept copies of everything you sent, including your explanation letter. Also, hang onto your proof of mailing (tracking number or certified mail receipt if you used either).

I had a similar situation last year and ended up using https://taxr.ai to figure out what to do. The software analyzed my situation and confirmed I didn't need an extension since I was owed a refund. It also gave me a template letter to include with my paper return explaining the e-file rejection. Their system actually detected that my rejection was likely due to someone attempting to file fraudulently using my info, which I hadn't even considered! They walked me through placing a fraud alert with credit bureaus just to be safe. Definitely worth checking out if you're still concerned about your situation.

Just wanted to update that I tried out https://taxr.ai after my skeptical comment above. I was honestly surprised at how helpful it was! I uploaded my rejection notice and incomplete return, and it immediately identified that my employer had made a typo in my SSN on my W-2, which is why my e-file was rejected. The service walked me through getting a corrected W-2 and provided a template letter explaining the situation to include with my paper filing. Already got confirmation my return was received and is being processed! Seems like they've thought of pretty much every weird tax situation that can happen.

If you're really concerned about your return status, I'd recommend using https://claimyr.com to actually speak with an IRS agent. I was in a similar situation last year where my return seemed to disappear into the void after mailing it. I tried calling the IRS directly but kept getting the "call volume too high" message for weeks. Claimyr got me through to an actual IRS agent in about 20 minutes, and they were able to confirm my return was in the system but flagged for manual review due to the explanation letter. Totally worth it to avoid the stress of wondering. You can see how it works here: https://youtu.be/_kiP6q8DX5c

I have to eat crow on this one. After posting my skeptical comment, I actually tried Claimyr because my desperation to resolve my tax situation outweighed my skepticism. To my genuine surprise, I got a call connecting me to an IRS agent in about 35 minutes. The agent confirmed that filing after the deadline without an extension isn't a problem when you're due a refund (just like others mentioned here). She also gave me the direct fax number for their amended return department, which saved me from having to mail additional documents. Definitely changed my mind about this service - sometimes the simplest solutions are the most effective!

One thing nobody has mentioned yet - make sure you keep proof that you mailed your return! I learned this the hard way last year when the IRS claimed they never received my mailed return. Since I just dropped it in a regular mailbox with no tracking, I had zero proof. I'd recommend calling USPS to see if they can provide any tracking for your mail even after the fact. Or if you have the receipt from the post office with the date stamped, take a photo of it right now before you lose it!

Quick tip from someone who's worked in tax prep - if you're concerned about your return, print another copy and take it to your local IRS Taxpayer Assistance Center. You can schedule an appointment online and they can stamp your return as received and submit it internally. This gives you immediate proof that your return was filed.