Will a future Spirit Rescue be done using the version of the Protocol in use at the time of the request, or perhaps a later version in use at the time of the client’s eventual transition?

It is the session done at the time of the request that is filed away and then brought to bear on the client in the future. So, in a sense, it is frozen in place in that particular version and cannot be expanded to incorporate techniques and processes learned subsequently that may be added later to the Protocol.