How to assign a skeleton with missing bones?

You wrote that you “can swap animations between the two, but not the mesh.” Try:

  1. Open an AnimSequence
  2. Select the “Mesh” tab at the top
  3. Select “Preview” at the top
  4. In the “Mesh Details” panel, under “Mesh/Skeleton” select the Skeleton you have retargetted to.
  5. If you have followed the previous instructions from the video and the linked documentation, you will see the other skeletal mesh that you want to change to.
  6. Select this.
  7. Now all the animations will preview with the desired mesh