GTA V Garage Bug Parks In Blockbuster Game Title
Multiple users have complained that after upgrading a vehicle or completing a mission and parking car in a garage in GTA V, the car will disappear entirely, or the upgrades will vanish. “We have received some reports about problems with cars and garages, particularly after upgrading and then completing a mission, and are looking into this now. Unfortunately, we do not currently have a workaround to recover a car if it is missing,” reads the Rockstar Games forum.
After looking into it, Rockstar says that the issue seems to occur if you drive another character’s personal vehicle. The company is working on a fix--there’s no workaround at this time--and it will email players when the fix is ready.

In the meantime, Rockstar’s advice is: “In the meantime, please try to avoid parking a car in a garage, driving one already in a garage, or getting in a default vehicle, when playing as a character other than the one with your upgrades.” Good luck with that.