I found out what was happening, the issue was not actually relevant to the hierarchy at all. I had meshes which had the same name as my bones. When the FBX was imported into unreal, it must see a mesh and a bone in the same file list, which is why it was renaming my bones. As soon as I renamed my meshes to NOT be the same name as the bone, all was good! 
Thank you for the thoughts on the matter 