Joe, call (518) 474-5282 Technical Services Bureau. They may scratch their heads as well. The other alternative is to go to the Babylon inspection facility (where mine was inspected) and ask the guys there what they suggest to do since they put them on in the first place.
They may ask that you go through the whole process again to get a NEW VIN if they don't issue dupes.
http://www.nydmv.state.ny.us/homemade.htm
Let me know what they say...I have the sticker in the same place and from what I understand, they are now agreeing to place the sticker on the bulkhead inside the engine bay. If this is so, and one can get a duplicate, then I'd get one myself and put the sticker in the bulkhead.
Cheers!