way too much personal info on the client and not enough information on the tax filing. You should not have been able to e-file the return a second time. If it was filed and accepted you would have received a reject notice that the return was on file. If you did not receive that and the 2nd filing was accepted then the original return was not efiled or not accepted. The accept/reject is from the IRS system. Also the fact that they got notices saying not filed also leads to an issue with the original return. From the efile homebase you can get the efiling history. 

To me it sounds like you efiled and it was rejected and you didn't see it - or you thought you efiled it and you missed it. I've done that - looked at the efiles the next day and say HEY they were here yesterday and signed why didn't I efile? Now I count the efile forms and I make sure I am efiling the same number of files. Stuff happens. Say sorry, efile it and offer to pay the interest.