So far every Lootr chest minecart I've come across in Enigmatica 6 has reset its inventory to its initial state after closing the inventory, leading to infinite duplication of its dungeon loot.
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If you aren't using version 0.0.4.15, please report this to the Enigmatica 6 developers as they should update the version available in the pack. A fix for this was released over three weeks ago.