Well, so I am using the avatar importer to quickly import these separated meshes from blender which had their own pivot (positions & rotations) and the results came out to be incorrect on the orientation while still maintaining the right position.
It seems like your objects are linked between multiple scenes or something like that.
I am not sure if this will solve your issue specifically but you can try this:
With the objects selected find the Make Single User > Object & Data button.
Also you may want to save your project before this, in case it does something you don’t want, since this will remove the links between scenes and you may want them? (Idk why you would have that though, never used/done it myself)