For Divine Divinity there is a collection of inventory files to replace items that people have lost, or that went missing due to a bug, etc. This procedure also works with Beyond Divinity, for the most part.
Lost Items - guide and directory of inventory files
(written for DD, works for BD)
see also For you cheaters out there (The Duplication Trick)
Note: In BD the items.000 no longer keeps track of the random attributes of equipment, so there is not the same morphing problem. However, when I tried swapping equipment in an earlier version of BD from late in act 1 to a new game, most of the items disappeared when I loaded the save and ran the cursor over them. I have not tried this with recent patch
In some cases a missing item may just be hard to spot, and it could help to hit the alt key or move the mouse cursor around any areas where the item could have dropped behind walls, or otherwise be obscured.
Below is a collection of zipped inventory files, mostly saved under version 1.44 and 1.45.
It is incomplete and this topic is unlikely to remain particularly organized. After enough inventory sets have been created to cover most problems people have run into, it may get redone.
(10KB) - from the room with a gargoyle statue and 3 keys on the ground, one of which triggers the appearance of a fixed teleporter stone that helps you reach the citadel.
My game was started in an earlier version and saved under 1.44 when I checked this. I tested in a save in act 3, and was able to give both characters a crystal bag (though with some irregularities in how game handles resistance boosts, since it is only expecting a single bag). It also worked fine when I loaded a previous save version, saved after passing the crystal bag, and did the file swapping to get it back.
Samuel's Lair keys
(10KB) - should be dropped by 2 of the DKs
(17KB) - the coal (Fergus' room), salt (citadel kitchen) and sulphur (gay medic's room) required to make a bomb to blow up the forge (one of the ways to leave act 1). In the hero's inventory, drag the salt barrel onto the coal barrel, then drag the sulphur onto the resulting coal & salt mixture to make the explosives.
(18 KB) - dropped by a spider to the north west of the imp 'hero' in the Spider Forest. The leg blends in a bit with the ground, so can be hard to see without using the alt key to highlight it.
Spore's antidote components
(17 KB) - the spider web piece from the queen spider's web and the mushroom extract from the imp farmer's house, required to make an antidote for the spores from the large mushroom in the mushroom forest, to revive the 6 imps.
(17KB) from a save after obtaining the pyramids in v1.41. There have been mixed results with people trying to get these by file swapping, mostly negative; see Missing Pyramid