If you opt for the snowball fight scene with Ciri after the battle of Keir Morhen, I found that this resulted in bombs vanishing from the lower bomb slot. In my case the snowballs automatically ended up being equipped in the lower bomb slot which had previously held superior Dimeritium bombs.

After this snowball fight scene had ended, I pulled up the inventory to once again equip the Dimeritium bombs but I found that they had vanished. Not only that, when I accessed the Alchemy menu it was as though they had never existed. I was fortunate that I had all the ingredients required to complete the manufacturing chain all the way back up to the superior Dimeritium bombs.

I would have expected that when the snowballs are automatically equipped in the lower bomb slot that any bombs displaced would have been returned to the main inventory, which was clearly not the case. I assume this to be a bug as at various times during the game certain items are automatically equipped in one the slots and whatever was displaced was returned to the main inventory.