My team was using the Unreal Mannequin for the base skeleton, I am using Character Creator 3to quickly create a bunch of characters and everything was going fine, until the animation team needed to add bones for their work in Maya/MoBu and update the skeleton in UE4. Now all my characters from CC3 are missing those extra bones and causing some animations to no longer work in Unreal. Even if I try to use the updated skeleton when I export from CC3 and import to UE4

How do I get those added bones when I export from Character Creator 3 to Unreal?

Ok I have pretty much the same question but for a completely custom skeleton that doesn't depend at all on the poorly constructed UE4 Mannequin.
Still working in Unreal, have a completely different skeleton, need to include custom auxiliary (like ik bones that are way simpler and better than the ue4 mannequin) and prop bones within the character, that are not skinned to anything.

Do you just need mount points to rig accessories to? You cannot change the mesh weighting of the body in CC3 to other bones, but if you add accessories attached to where the new bones you need are, then it might work.

Not sure if this will work for you, but an accessory essentially can be thought of as a mount point, or bone stub.

Import an accessory. I used a simple cube.
Name the cube to the name of your new bone.
Change the attachment point to the proper parent-bone in the modify panel, accessory section.
Select the accessory and open the edit mesh tool.
Hide the mesh of the accessory and close the tool.
Export, making sure to select the "Delete Hidden Mesh box".