Before any election results are considered final in NY (or any other state), every soldier from there should be accounted for and their ballots counted. If their votes are not going to be counted, the whole election should be declared invalid and done all over again.
Some states have been granted a waiver for the MOVE act and that waiver might be worse than the violation because it includes no prior registration and an extended voting period. So, potentially, as many votes as necessary could be drummed up after the election is already over.