To recreate the issue:
Go to personnel
Select any soldier
View that soldier’s inventory
Highlight all soldier tabs on the left and view all equipment.
Then start dragging lots of different items to the box that scraps items. After you do this 5-10 times, suddenly a portion of your inventory will just disappear (other than the items you have purposefully scrapped obviously).
You can avoid the issue, if you are careful to back out after every 2-3 item scraps. When I first ran into this issue, I lost a lot of gear I had crafted for my soldiers, but hadn’t equipped yet.