I just had an entire drawer (4 slot oak, full block) which was locked and had the obsidian upgrade and the level 2 status upgrade. When I rightclicked that one with a stack of 3 sorting upgrades, 2 of the sorting upgrades vanished, the whole block got deleted (including all the contents).
This is replicatable.

MC 1.7.10, Storage Drawers 1.7.2.

Thanks, I'll try and look into it this weekend. The refined relocation bits are tested pretty lightly.

Fixed in 1.7.4. The bug was applying a sorting upgrade to a sorting drawer (the hint was that you said 2 upgrade vanished -- maybe it registered a double click).