Originally Posted by acidhouse_
4. First you should tell to Blender, that this is the original position of your skeleton-model. Please push Ctrl A. This is applying rotation. This means, that now all the rotations of the bones will be "0,0,0", so if you push later Alt R (clear rotation), you will get this position. (Please turn on numerical menu (N), to see what happens when you make this apply rotation command.)
5. Select the whole skeleton-model again. Go to edit mode. Then push A, to select all the bones. (They should be yellow now.) Then say Ctrl N, and I am sure you will see all the axises will be changed to stay on the same way.
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