I have not tested this with any other material weapon, nor have I noticed it happening with tools.
I have created three diamond swords that have all vanished from my inventory, all of which are unenchanted.
Starngely enough, the original sword I made and enchanted (sharpness IV) and kept aside for repair has not vanished and is down to only a few uses left.
39th Duplicate of MC-15416, please use the search function to see if your bug has already been submitted. Currently over 56% of tickets are being closed as duplicate.