Multiple skeletons created when importing animation with custom handles?

I have a custom rig set up in Maya 2016. It has custom handles created from nurbs curves that act as controllers for the skeleton. These handles end up as part of the hierarchy in Maya. Whenever I export the animation to Unreal, Unreal thinks that each bone after a handle in the hierarchy is a new root. Therefore it creates multiple animations from each root. The rig I have is quite complicated so I end up with roughly 15-20 different skeletons.
Is there a way to make Unreal include these nurbs curve handles in the hierarchy without creating new skeletons?