Yes you should lose all bones. You more than likely will have to paint skin weights also. Its easier to retarget an animation in something like Maya Lt. If thats truly what you need to do. While keeping your character intact. Then you can have character interactions like blinking for example. You can also layer, and retarget them in unreal. Using a mixamo only character is actually a good bit of work. I rig my characters to UE4 skeleton. All of them. If I need a facial rig. Than I parent it to the UE4 skeleton. As there is a whole lot more content already blended in ue4.