STOP WHAT YOU'RE DOING AND READ!
Something don't look right, don't panic, relax, and restart!
If you find something missing when you load into online, DON'T DO ANYTHING ELSE! Shutdown your console and reload the game, they will reappear. Now, if you did not follow these simple steps, left your apartment/garage and did other things and the game eventually saves, you're screwed.
AGAIN. Something don't look right, don't panic, relax, and restart!
This also goes for missing characters, don't spam retry, don't make a new character, don't panic, don't do anything, and restart console.
Never lost a single thing since launch due to the above.
Don't fall victim to shoddy Rockstar servers EVER AGAIN!
For people that have lost characters, cars, apartments permanently. don't give up! Rockstar is looking out for us and there are signs of them having a backup database and working around the clock to restore your sh*t.