I'm stepping out on a limb here, but after Texas seceeded and began preparation for the Sibley Campaign, there was discussion that secession voided all previous arrangements/aggrements between the Republic (and State) of Texas and the Federal government. That would include a return to the original Texas boundaries that, among other things, included the eastern half of New Mexico---including Taos. I don't know if the unit you are discussing might have had an agent in the area, but stranger things were happening about that time.

Mike