WOW. Just noticed after all this time that inventory items just dissapear! Especially when transferring back and forth between companions. AND YES, I am aware that companions will drop items, and also equip them, and NO this is not what is happening, and NO I am not trying to sell them to someone who won't buy the stolen goods. I transfered 4 laser rifles to Boone (stolen from Silver Rush) and when I left the building, they dissapeared from his inventory! I have since tested with several items, and it appears stuff just dissapears whenever it wants to, and worse, sometimes a companions inventory shows that it has one of something, but really there is more then one, as evidenced when you try to return the item to your inventory.

Again something else we need to add to the list, however as of yet I haven't been experiencing this with cass

Ok, Noticed something else. Had a fully loaded Plasma Rifle in my inventory, and a 50% CND plasma rifle in Boones inventory. When I moved the one in his back to mine, my inventory only showed one item, and it was the half CND rifle. Looked like I had lost my full one, HOWEVER, when I dropped the one from my inventory on the ground, the fully CND one reappeared in my inventory! BUT when I sold the 50% CND one from my inventory, it sold both it and the full condition one. So basically, the game is not managing Quantities well. Must be a bug with the new companion inventory system. Feels like just another amateur programming mistake.

More testing discovered that the items that seem to dissapear from inventory are items that when dropped, require you to steal them when you pick them back up. So what appears to be happening is that when you steal some items, they dont actually register as having been stolen and now belonging to you, so they just dissapear from your inventory. This is NOT a doubling up of items, I know how many items I stole and how many I should have. It just seems that they are not registered as having been taken by you. Perhaps this is because I moved them to my companions inventory before moving to another area?

Even though the item shows "Steal" when you drop it, there is no karma hit when you pick it back up. The trick is to drop all of the items of that ty[e, pick one up and a time and sell it. It appears if you sell all the ones that still register as needing to be stolen, the inventory straightens itself out.

I came out of Gomorrah and Boone's rifle never came back(although I'm not 100% sure he had it before). It might of disappeared like you guys are saying. Now when I equip him with any gun he never uses it and just uses his fist despite toggling melee and ranged. Super annoying and it just makes him useless.