Have seen a number of report from others about the same thing happening, also with ProConnect Tax, but this doesn't seem to be complaints on other forums from users of other companies' tax programs.  Not sure if these are isolated problems with Intuit's systems.  You may like to call Intuit Support in the first instance to have them look into these returns.  Otherwise, respond to the notice with a copy of the return they requested along with the e-file confirmation as proof of filing.