Are the free-floating memories also deposited in the thought plane and thereby covered by the new Protocol step requesting its healing?

This is the case and this is the reason also that intuitively, there were no stirrings and you were comfortable and feeling everything is attended to. You can note that in your manual, but it need not be stated explicitly in the requests for Thought Plane Healing—as the healing will be comprehensive for all aspects, components, and types of energies present.