Unity's Editor extension for merge atlas meta(bones, sprites regions and so on). Very useful in collaborating work with other artists on the same project.
You can merge metadata from two atlases in one of them. In meta stored: sprite regions, sizes, pivot points, bones, meshes and bone weights information.
Also, it can fix all links in prefabs and scenes. Fix missed sprites in prefabs or change from one atlas to another.
2) Add all assets via explorer. NOT IN UNITY EDITOR (it is replace all GUIIDs).
3) Then add extension MergeAtlasMeta in that project and run it. Add atlases in texture place.
4) Open extension and tap GET METADATA. The extension will find all assets that use it and the difference between them.
5) Then you need manually click each sprite that you need to migrate.
6) Click UPDATE METAS. Note: If in both atlases you have same sprites names extension will rewrite it.
6) Then you need open prefabs parts and click each prefab or scene that need a switch from one atlas to another
7) Done copy update assets (prefabs, scenes and atlases meta in work project).
Check console if you have same errors. I'm trying to do it in a live project but unity blocked metafiles to write. In a new project, all work great.
You can move sprites with bones after migrating without problems, bones will work as usual.