I also have this issue and even transferring the files directly over to the UE4 mod folder and renaming as they should be (following instructions from a dev) and the game merely just deletes them once it loads up. Doing so the Pyrix mods were listed as being from a different version of the game and I was asked to load or not. Although it made no difference the game would delete anything I put in the UE4 mod folder as soon as the game loaded up.