I don't use Unreal Engine, but it seems some people get it to work while others don't, so I'm not really sure, but that's what the FBX and FBX Alt files are intended to be for.
Viewing post in Unity Sex Animation: Rough Pack comments
If half of the bones are flipped vertically, there isn't anything you can do(beside try rotating them), that's just how the animations got exported from Unity, assuming you're talking about the FBX[Alt] files. The animations should still work even though they look weird, if not I'll see if I could fix that.