If you drag a stack into (or out of) a container or your inventory (or between 2 inventory windows), and hold down the control key before dropping, it will bring up a split stack pane, which will let you specify how many to transfer.
Do you have any recent saves you can check to see where the problem occurred? As long as you didn't loose anything there is not really any reason to reload, but if you don't have much to redo it would probably be safer to do so. I'd guess the problem was during the act transition, when the game removes any BF keys that you have picked up, etc from your inventory.