I think this is regarding the new Craft Bench Upgrade to GS 500, where it require you to spend a weapon & gear with GS 490+ (or GS 500, i dont remember). So Mudl92, you need to spend that items (weapon & gear), similar to recalibration, where it destroys the item. And since you had it equipped, it couldn't destroy. You need to have a spare weapon & gear that is not equipped (and may be not in loadouts & favourites as well) to actually upgrade the craft bench.
I think the information provided there wasn't clear enough. Might need some copy change over there.