Rockstar has acknowledged an issue with upgraded cars in Grand Theft Auto V not saving correctly when parked in garages.
“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,” Rockstar said. “Also please note that vehicles saves in the garage of one safehouse (Franklin's Aunt's) may not show up in the garage of a different safehouse (Franklin's Vinewood Hills).”
In an update, the developer said that the issue might occur when one character drives another’s personal vehicle.
“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.”