If you create repeating command block that keeps replacing slot in player's inventory with item, then deleting this item through 'Destroy Item' slot sometimes makes it not appear again (Even though in player's data you can see that item in that slot).

This fixes on its own, when you rejoin world, die, or try inserting other item in that slot (in the last case, item you tried inserting gets permanently destroyed)

You can see all this in video I attached (sorry for low quality, but the size limit here is only 10 Mb...)

In case this wasn't obvious, at the first time sword re-appeared I middle-clicked (picking up grass block).

Command to reproduce bug (in repeating command block):
execute as @p run item replace entity @s hotbar.0 with minecraft:diamond_sword 1