This worked for me, give it a shot:
Trying to return the vehicle to stock in the normal manner will fail, but I can return it to stock tune by: trying to again download a custom tune, turning the key off as it updates (resulting in a download error), the tuner asks to return to stock, I accept and the update works successfully. The car will then start, on the stock tune.
Mine: 2004 Subaru WRX Wagon: 116k, WRB
Gone: 2002 SVT, #1654
Hers: 2012 Focus Ti Sedan: 67k, SGM, Manual