Update September 22, 2013: Rockstar has identified a possible cause for this issue: “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.”
Okay, there is a lot of discussion and confusion out there regarding vehicles that are randomly losing upgrades or are simply disappearing from garages. Not sure if this is good news or bad news, but Rockstar is aware of this issue and is apparently working on fixing it. Folks, it looks like we’re headed quickly to Patch #1 for Grand Theft Auto 5 on Xbox 360 and PlayStation 3. Here is a quote from Rockstar on their website:
“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.com
I would imagine this is a high priority bug in the game and a resolution should be coming very soon. We will update with news of a fix. Until then, I suppose we all just have to deal with a bit of random disappointments regarding our beloved vehicles.