I just discovered this. Played pretty much all the way to the end of Act 2 with the same party. Celebrated by going to the stronghold to level everyone else up, swapping them in and out of the party by the bedroom upstairs in Brighthollow.
Merrily carried on and then needed to fish something out of the inventory in Nine Elms. Found all my pets are gone. All of them. Even the Miniature Giant Space Piglet I got as a KS backer...
I'm seriously hacked off. This might not be a "gamebreaker", but it's just taken a dirty great sledgehammer to my enjoyment of the game.
It's great to hear that there might be a patch to fix it, but will it correct the mistake? Will we be allowed to add back missing items without triggering the Steam Achievements block that using the console has? Can I get my MGSP back?