A recent post from Rockstar Support has stated that they are aware of the problem and are looking into it, although they do not have a workaround for it at the time being. They do however say that “This issue may occur if you drive another character’s personal vehicle. We are looking into a fix to prevent this from occurring in the future.”
Vehicles disappearing from the GTA V garage, or losing upgrades
Question: I upgraded my car and then completed a mission, and now my car is gone. Help!
Question: I’ve lost some of my upgrades after completing some missions and then checking my garage. What should I do?
Answer: 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. If you would like to receive an automatic email notification as soon as there is more information, please log into the Support Site and click Subscribe at the top of this page.
Also please note that vehicles saves in the garage of one safehouse may not show up in the garage of a different safehouse.
Update for 9/22/13: This issue may occur if you drive another character’s personal vehicle. We are looking into a fix to prevent this from occurring in the future. If you would like to receive an automatic email notification when the fix is live, please log into the Support Site and click Subscribe at the top of this page. 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.
source [Rockstar Support]