I've found a glitch with the crafters, but only with Project E. If you set up a crafter to repair an item with covalence dust, then view a another crafting table with a recipe for repairing another tool the output gets replaced with the item output from the other table.
Essentially:
Set up a Crafter to repair a stone hoe using Covalence Dust. Ouput should be stone hoe
Look at a crafting table/bench and repair diamond armor with covalence dust. Output stone hoe on crafter is replaced with diamond armor, and the machine will continue to output diamond armor so long as it has the resources to repair stone hoes with covalence dust.