Mesh is flipped thanks to bone but armature is working

Hi,

I am a bit new to 3D but got lots of experience with game development.

I have a textured character model that I imported from Blender, it was working perfectly... except, I ran into some problems when parenting other objects to the skeleton. The objects got attached to the wrong end of the bone.

Ex. Hair got attached to the bottom of the head instead of the top of the head.

I flipped around the bones in Blender (did something similar when rigging the character). Everything was working fine in Blender but the mesh that is associated with the changed bones now appear flipped in Unity.

Ex: The head is upside down and looking backwards.

The armature is on the other hand working perfectly fine with mecanim, animations etc. There seems to be some connection between bones and vertex groups somewhere but I cannot find it and force a recalculation or edit it so that the head appear the correct way.

Has anyone else experience with this kind of problem? Did you have to flip around a bone and how did you get the mesh to appear correctly in Unity afterwards?