This is how I explained it to someone else with the same issue and they were able to resolve it and Efile the 1040X

Let' s say you have a client file named  SmithJohn.19i that needs to be amended.

If youre going to make a copy before amending (I never do, I just save a printed or PDF of the original, its not correct so I dont see a need to keep it as a computer tax file) then the copy you save should be something like SmithJohnOrig.19i and uncheck the EF boxes on it.

Then use the same file that you Efiled originally SmithJohn.19i to create and Efile the amendment. 

That way the program recognizes the original as being Efiled by you and also, when you roll the file into the 2020 program next season you're still using same the SmithJohn. tax file that has the correct info into the new tax year.