Note: already posted on facepunch but I figured I'll post here as well as more people know stuff about shapekeys/flexes

I posed a ported model, which has flexes, as close as I could to a TF2 character, but the issue now is I can't set its rest/reference post to be this current pose.

Trying to Apply Pose as Rest Pose fails as the mesh doesn't update to the new pose.
https://files.facepunch.com/forum/upload/111014/5457fb06-1af2-4046-9e4f-859dce787677/image.png
Trying to apply the Armature modifier in an attempt to fix the above issue also fails due to this error:
https://files.facepunch.com/forum/upload/111014/91ec5e21-aae5-4589-aabc-070c177378e6/image.png

Is there any workaround I can do (such as a plugin)? I must keep the shapekeys, so deleting them is not an option. Seperating the head is also not an option as I have adjusted the head/spine bones.