Is it of any value to request during a Protocol session to have a member of the spirit team give the subconscious mind of a client regular positive affirmations as encouragement?

There is nothing wrong with this, and it can be helpful. The problem truly, is knowing where and when and what to say. This is very broad-based, very general, very vague, and will have very modest benefit at best. Life is complex, there are many moods, many emotional ups and downs, many situations that come and go, all of which activity demands action or a response of some kind, to sort and sift through the meaning and the response, if only internal. With no specificity of what to deliver, when to deliver it, how often, under what circumstances, and then being quite limited to something quite general, or specific but yet which may not match at all any given circumstance in a way that can provide true help other than just a pat on the back, the value for this is quite restricted and is not truly worth the energy needed to implement the suggestion. Any request for intervention by the spirit team is best done to deliver deep healing in some way. This might include having a dialogue with the subconscious to be revealing as to its motives, and mood, and beliefs in the moment most governing what the mind is addressing, followed by a request to administer healing for negativity that is expressed, will be much more likely to be timely and a benefit in changing the course of the person’s experience to the positive.