Lost installed improvements, lost changes (XCOM 2)

Recently noticed, which actually freaked out and deleted the game after the missions my soldiers are lost implanted modules improvements, not all, and one of the two, and not just roll their installation, but it is gone, there is no slot in the inventory. Was a mod that allowed you to choose AVTS perks(which are randomly given compartment due some) So they, too, disappear or change, not all but one or two. Often happened, that was customized a soldier was preserved in a save slot after that, then uploaded it and the changes were rolled back.

Someone faced with similar? This is a bug of the game or fashion? I just put visual mods on his tattoo, pistols-machine guns, katana swords and new helmets. No mods on perks, no mods on the gameplay, nikakih of longbarrow and counters, only guns helmets of tattoo. All of the nexus.