I made a model with armature and animations.Everything was working fine in unity but axis y and z were swapped. So i went back to blender and tried to apply rotation but it totally messe up model. Im not sure what exactly "rotation to deltas" does but i tried and it seems like rotation was applied correctly but i axis are still wrong in unity.
The correct way to apply a pose of a rigged character is: pose the model in its desired rest pose; select the mesh and apply its armature modifier; select the armature and in pose mode select all bones and press Ctrl A "Apply pose as rest pose"; add to the mesh a new armature modifier, pointing a the armature rig.
This procedure will not affect the weights, but can destroy any previously made animation.