I have one mod that takes inventory items and puts them on hot keys Z, V and B for instant healing....it also puts my worn armor on a separate inventory to free space in my own. It works great and the extra 8 inventory slots are a huge benefit. Unfortunately this benefit creates additional inventory slots to hold these items, and when I disable the mod the slots disappear with all those items. When I re-enable the mod they do not return.

I have to remove ALL inventory items that are in those locations back into basic inventory. Since the armor items are worn, I have to take all armor off before I disable the mod. I can then re-equip the items after I login vanilla.

Be aware that the same thing will most likely happen using any mod that increases inventory or chest size as the vanilla game has no place to put those items.