First of all, let me say that I'm a fellow user--not a tax person. So I'll tell you some of my "thoughts", and others may also add to this thread today. But I'm not giving any legal advice or tax advice.
First of all, don't get too worried, in my opinion. I doubt you will be in any "trouble". From what you've said, it was a mistake--not willful tax fraud--and you said they are identical. I'm surprised your tax preparer used the terms "tax fraud" and "jail" to scare you. The IRS should recognize that you have filed twice by both methods. They might contact you with a letter and ask you about it to clarify, in which case you can respond and explain to them what happened.
In my opinion as a lay person and fellow user, there shouldn't be any penalty for an error like that. But if both returns start processing, the IRS might delay or freeze your refund until that can be cleared up. Or it's possible they complete the efiled return and actually pay the refund before they process and realize the paper return is a duplicate. In that case they may still contact you by letter to explain why a second return was filed.
The IRS will begin processing whichever one they received first. So if your efiled return was accepted, it will likely process before the paper return. If the paper return had processed to any significant degree, then the efiled return should have been rejected as a duplicate. So if the efiled return was accepted, it sounds like the efiled return began processing first.
Did you efile the return with TurboTax? If so, and if you used Online TurboTax, you can log into your account, and at the Tax Home it should tell you whether it has been accepted.
You said it's "currently processing", so does that mean you have found evidence of such in the IRS "Where's My Refund" tool?
https://www.irs.gov/Refunds
If the efiled return was accepted, then it is already in the IRS system, and "normally" would be processed within 21 days. It's possible that if they receive and begin processing the paper return before the efiled return has finished processing, that they may put everything on hold until they contact you for an explanation.
At the moment the IRS is not currently processing paper returns due to Coronavirus, but I don't know if that means they are not even entering them into the system. But with many IRS employees staying home, that may be the case. Paper returns may just be sitting in a mailbag for all I know.
Even in the best of times, it normally takes at least 4 weeks for a mailed return to show up in the "Where's My Refund" tool. So the fact that you didn't find it in the WMR tool when you first tried would be normal, since it has not even been 4 weeks since you mailed it. So even in normal times if you had been able to reach the IRS by phone, they probably wouldn't have been able to tell you anything about a mailed return prior to 4 weeks from mailing. In fact on their website they say not to phone them before 4 weeks after mailing.
Since you were able to successfully efile the second return, I'm curious as to why your tax preparer did not efile the initial return in the first place and thus avoid all this. Why was your initial return being filed on paper in the mail? Did the preparer not have the ability to efile it; i.e., was the preparer not an authorized efile provider?
