the .reuse() and .transformDamage() methods does not work with recipe stages,
for both mods.recipestages.Recipes.addShapeless() or mods.recipestages.Recipes.setRecipeStage()

https://pastebin.com/MeeHDTeP
(see bottom of code)

Crafttweaker log please

This is the crafttweakerlog:
https://pastebin.com/UCf2ECjZ

Test code used for this log:
https://pastebin.com/XddNESWA

Attached full log:
crafttweaker.log

theres no crashes, but the tool item used in the recipe disappears after crafting.
it should be left in the crafting grid with durability consumed a bit (if used the craftingTable.addShapeless() method and no recipe stages added)

Thanks for the report! This one totally missed my testing, should all be fixed now :)