It basically means that Reacher and Peterson came to a decision at the same time, but did not say anything to each other, it was just understood between them ( perhaps through facial expressions, body language, etc ) and they were going to save what they had to say to Janet at a time when it would mean the most or be the most valuable ( when it counts )

We can break the sentence up. Maybe you can understand it better: 1 - Janet Salter began to relax. 2 - Reacher and Peterson took a mutual unspoken decision to save it for when it is going to count. I'm guessing you do not get part #2? It means that Reacher and Peterson both took the same decision without talking about it, and that decision was to save "it" for when "it" can be used better.