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I enveloped a character mesh to a skeleton that I changed from the SWBF skeleton so it would fit better. Then I changed the rotations back to the SWBF skeleton using ZETools apply animation to hierarchy. I also changed the bone lengths back manually in the property pages. Now the character mesh has the same pose and proportions as standard SWBF characters.

The problem is that it doesn't look right ingame with what i should be seeing. When I selected "Set Reference Poses" the character mesh (not the skeleton) went back to the old pose. Same thing when I try to mute the envelope operator. Normally I would mute the envelope operator and then set reference poses but that is not working.

Any Ideas to fix this? Or is there another way to do what I am trying to do? I can provide pictures and more info if needed.

EDIT: I learned that the deformers (bones) are not in rest pose. But I don't know what to do with that, since it wont let me by setting a new ref pose.

EDIT: One solution is to press freeze, set the new pose ref pose, then re-envelope from scratch. But that seems unnecessary.

MileHighGuy wrote:I can provide pictures and more info if needed.

Yes please. I'm not entirely sure what you're doing.
When you make changes to geometry you need to freeze it. Reference pose data isn't passed on to the msh format. There is really no need to mess with it unless you are checking weighting or animating. It kind of sounds like you're working against the grain here.

I'll post pictures. I had made a custom skeleton for a model with different proportions. I just tried to get the proportions back to swbf by changing it back to the normal skeleton (making the arms shrink by changing the length of the relevant bones).

Edit: pictures incoming

EDIT: hopefully this explains it better:

http://imgur.com/a/D07Gg

You should take what you have in the first image and freeze the mesh, set the envelope, key the bones in their current position and export a new basepose.

I have done that already, but it did not turn out so well (its set up that way in the 1st screenshot). the problem is that with the new basepose the animations get messed up because the arms are so long compared to the stock basepose. For example when the unit used a rifle his left hand would be way off the the side, not holding the rifle. That's why I am trying to do this.