Up to now I've never had a issue with cars passing inspection with a blank or non matching vin. Recently I've had this issue occur. Problem is immo3 EEPROM with blank or mismatched vin will fail only immo3 EEPROM tho. I did a narrowband to wideband conversion on a 2000 mk4 1.8t used a awp Ecu, flash file and EEPROM with blank values and it still failed inspection even though in 2000 imm02 didn't have the vin strored in the EEPROM. Ie found 2 ways to solve this issue. Use the EEPROM from the immo2 narrowband car and immo off in flash or use immo3 EEPROM and patch the vin. I've verified both methods as working.

I know this is probably guarded info, but can you share how to do this? 

Yes but I believe the VIN is stored in 3 locations in the EEPROM only one of which is in the unencrypted portion of the EEPROM. It seems the OP has a way to change all the references to the VIN so I was wondering how that is done?