When pulling enchantments off my Flux infused sword (which by default is unbreakable as long as it has power) was destroyed in my auto dis-enchanter. I have had no problem with it doing this before as i have reconfigured the enchants quite a few times. Sadly this also disappeared with my only looting 3 enchantment so i guess it is back to the drawing board. sincerely, metalobism
Try to reproduce it with the latest version of the mods and if you can reproduce it report it to the mod author.
It is supposed to do that. It's not a bug. Almost all enchant removing machines do this. Examples are the MFR disenchanter and the Draconic revolution one. Things like the spelbinding cloth from thaum doesn't destroy powered items (used to destroy non powered one, not sure if it still does) but it deletes the enchantments. (this is better to "redesign" the enchantment of powered items when the user isn't happy with them.)