It is possible to throw an open alchemical bag on the ground/move it in the inventory, while the GUI is still open.
Any items that are then put into it are lost, any items taken out are duplicated...

I think this functionality will get added, seeing as the bags are still WIP!

Most mods simply deny editing the slot the bag is in...
I currently don't know how to achieve this without looking into their sources.
So unfortunately you have to figure that out ;)

I want to add something to this. When you move items from the bag in your inventory and close Minecraft the items will be duplicated too. SlotAlchemicalBag#onSlotChange does not seem to be saving anything (or maybe it isn't called?). I'll investigate this further.

Found cause and fix for these issues. Will PR the fixes in a bit.