So I am almost certain based on my own experience and from what I have been reading that the character delete glitch is caused when you leave a game when the cloud is down.
You exit out (even if you exit to single player) and the game initiates a autosave, but since the cloud is down there is no where for your save to go and thus it's lost and your character is lost.
Now for some Q&A
Q:How can you tell if the cloud is having trouble retrieving my character or if it got deleted?
A:If you try to join a online game and your character doesn't appear, either it's gone or the cloud cant retrieve it at the moment. To check, go to rockstar social club and check to see if your stats appear. If they do then you are fine you just need to keep trying till the cloud starts working again. If they don't, your character is gone and there is nothing you can do but hope R* can restore it.
Q:My character got deleted. Should I make a new one?
A: NO. If you do make a new character whatever is left of your old one will be wiped for sure and might prevent R* from recovering it at a later date.
Q:How can I prevent this?
A:Since there is no way to know if the cloud is down while you are already in a online game, there is no way to know if your character will be saved when you exit. The only surefire way is to not play until R* fixes the issue.
Hope this helps to clear up the confusion.
Update:For anyone who lost a character, if you get on the iFruit app and check the Los Santos Customs mini app your cars are still there (mine are at least). So it seems that not all of our data is lost and it may be recoverable. Just some info to give you guys a little hope.