When you finish editing a level instance, the actor is converted from the world position to the local position of the level instance, but if you replace the actor, the conversion process is performed by retrieving the original (marked for deletion) actor from the package, not the new actor.
The following workaround that removes the old package from PackageMap works.
see video [Link Removed] for detail
The replaced actor moves to wrong location
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-159517 in the post.