No you can't use the OBC numbers directly to manually program the remote. You need to use EFCs. But you need to have a corresponding setup code that has the correct IR protocol, and device number(s). Please post a link to the CCF file. Then we'll see if the 6050 has a suitable setup code that can be modified.

Edited to Add:
The M-VR600 uses the Mistubishi IR protocol, device 119. The setup code that sends this is Audio 1393. I suspect that this may have been added as a custom feature for the Mitsubishi remote, so depending on what you did, the setup code itself could have been erased, or (more better) the setup code has been mis-assigned. It is also possible that the setup code is some other number, but 1393 is used in a number of remotes made by UEI (OneForAll, etc.)
Try assigning Aud 1393, and see if the remote blinks twice. If so, I expect Vol, Mute, and Power to work--maybe everything.