So i had this problem a little while back where i couldn't export blend shapes with my animation from a referenced rig file. I was still able to get the animation file exported correctly but i had to copy all my animation to the main file to make sure all the blendshapes got exported. So I'm curious if anyone knows why blendshapes won't export from a referenced file.
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I've recently had this issue. Did you ever find a cause/solution?