Okay, so I'm not entirely certain if this is a bug in this mod or in Inventory Sorter, but it's definitely a bug in the interaction between the two mods, as I've isolated when I turned off all the keybinds for Inventory Sorter.

What happens: alt/shift/ctrl + middle clicking to sort your backpack will cause all of your overloaded stacks (from using the stack upgrades) to expand out into the normal stacks, potentially filling your backpack slots with all the expanded stuff, and voiding/deleting everything else.

Pre-accidental clicking (You'll notice full stack of gold and netherite in particular):

The results of the accidental click:

Post-resorting (of particular note is the much small stack of gold and the complete loss of the netherite):

Now, as I said this is definitely from an interaction with the Inventory Sorter mod, but it was completely unexpected (since I didn't even KNOW that alt/shift/ctrl + middle click was a thing, and it doesn't do anything in a normal container it seems, which is kinda why I'm reporting the bug here).

versions:
Minecraft 1.19.2
Forge 43.1.3
inventorysorter-1.19.2-21.0.1
sophisticatedbackpacks-1.19.2-3.18.24.703

Somehow I completely missed the issue over on the Inventory Sorter github (cpw/inventorysorter#123) that is causing this very problem. Guess I'll close this puppy as a derp. Sorry.