I had the legendary bleeding gorilla arms mod and that vanished while installed to be replaced by a Physical Damage mod. I installed the electrical damage mod for the gorilla arms and that too was changed into a Physical Damage mod. I now have three Physical Damage mods in my inventory but no bleeding or electrical damage ones. Not sure when it happened so can't roll back saves to see. Given that it happened twice it can't be a one-time thing. Both mods were installed at the time of them being changed to Physical Damage mods.