I'd suggest going through the process a little differently by creating the second mesh (the one with just the scabbard) in OpenBRF itself.
- Export the original mesh like you would normally.
- Import it in OpenBRF.
- Create a copy of the mesh (ctrl C, ctrl V).
- Right-click the copy, and select the "split mesh into connected submeshes" option. Again, I'm not at a PC with OpenBRF so I can't say how many submeshes you'll get.
- Select all the submeshes that make up the hilt of the sword, right click, and select "combine meshes". Delete the smaller submeshes afterwards.
- Do the same with the scabbard. Now you should have two submeshes: the hilt and the scabbard.
- Right-click the hilt, and select "Roto-translate-rescale". Scale the hilt down to like 2-5%, and move it into the scabbard.
- Combine the scabbard and hilt submeshes.
- Make a copy of the combined mesh. You should now have the original mesh (with the sword in the scabbard), and two copies of the mesh that look like they just have the scabbard.
- Combine the meshes as a vertex animation.
That should fix any import/export issues that could interfere with the vertex animation, as you ensure that you use an identical mesh for all frames.