I had to amend a return for a client who got a revised W2.  Only thing that changed was NYC tax (Federal and State were fine).  Getting fatal diagnostic "Form 1040: Form 1040-X is included in this return. This return must be e-filed as an amended return. Please use E-file Amendment options in the File Return.".  

I checked the Federal Amended Return, even though no changes, and filed that and it shows received but I dont know what to do to clear this fatal.