The thing is, I don’t really know what’s the problem. Something happened to bones structure of ‘Skeleton Deformation’ layer. It throws the infamous “<bone> is missing link” error like so:

The XML section of the ‘Skeleton Deformation’ looks like this:
<layer type="skeleton_deformation" active="true" exclude_from_rendering="false" version="0.1">
<param name="z_depth">
<real value="0.0000000000"/>
</param>
<param name="amount">
<real value="1.0000000000"/>
</param>
<param name="blend_method">
<integer value="0" static="true"/>
</param>
<param name="bones">
<static_list type="pair_bone_object_bone_object">
<entry>
<composite type="pair_bone_object_bone_object">
<first>
<bone type="bone_object" guid="D8C6A54B7AE6416E03DDE03707B68FC8"/>
</first>
<second>
<bone type="bone_object" guid="FD4245C71EB51C3BB53001CE14EE3F04"/>
</second>
</composite>
</entry>
<entry>
<composite type="pair_bone_object_bone_object">
<first>
<bone type="bone_object" guid="8270FABEB8BC6759CA9B579A79E0EE49"/>
</first>
<second>
<bone type="bone_object" guid="86990EC59CEC5813E778EF3397C30209"/>
</second>
</composite>
</entry>
<entry>
<composite type="pair_bone_object_bone_object">
<first>
<bone type="bone_object" guid="3553E9DA587B5695B38D6C1434A02CB5"/>
</first>
<second>
<bone type="bone_object" guid="DA6DFA424A37439651BB5365A3369BBE"/>
</second>
</composite>
</entry>
</static_list>
</param>
<param name="point1">
<vector>
<x>-4.0000000000</x>
<y>4.0000000000</y>
</vector>
</param>
<param name="point2">
<vector>
<x>4.0000000000</x>
<y>-4.0000000000</y>
</vector>
</param>
<param name="x_subdivisions">
<integer value="32"/>
</param>
<param name="y_subdivisions">
<integer value="32"/>
</param>
</layer>
Seems like bone is referencing to some GUID which is missing. I guess it’s because it was copied? Maybe, but I recall people having this problem somewhat randomly (was working fine, but then broke after save/reload).
If you got confused by the word “fixed” I used, then sorry, I didn’t really “fixed it” more like amputated damaged parts (deleted all skeleton deformation layers).