Just happened to me. Thankfully I had a manual save and will only have to backtrack a little bit in the story.
I jumped straight to online from the game load up screen, played around a bit, and jumped back to story mode. I chose Trevor and woke up drunk in a graveyard (HAH!).
I then did a certain freak mission.
When trying to access the wheel... everything was GONE. I was confused and thinking this was part of the mission for some reason and my stuff would come back. I tried to go to the safe house to save (glad I didn't now) and I ended up playing through another mission. After it was over, my weapons were all still MIA. Switch to Micheal... no weapons. Franklin... same story. Loaded my manual save and the weapons are back and I've lost progress mentioned above. So I have about an hour of work to redo.
Be wary! I'm gonna send R* a heads up.