@tpaulrazvan: It's probably better to address such questions to a blender community. From what I understand you have body mesh, head mesh and usual animation for body - and that animation doesn't work properly for the head, because eyes and mouth are supposed to be animated separately with FaceFX animation, that's why respective transformations are not present for eye/mouth bones.
After brief search I found out that UDK may include free version of old FaceFX 2009, which allows to work with FaceFX assets exportable from umodel (if possible) and convert them to more appropriate formats. For example, it's mentioned
here,
here and
here, though in our case animset files are UDK assets, not FaceFX. But third-party solutions like that are mostly out of scope of the forum.
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