Complex sentence: The new governor, Manuel Armijo, was in office when Rowland and Workman were arrested for smuggling which although a common pastime may have been retribution for their feigned loyalty to the Taoseño revolt.
Split into simpler sentences: The new governor, Manuel Armijo, was in office when Rowland and Workman were arrested for smuggling. This was a common pastime, but the arrest may have been retribution for their alleged loyalty to the Taoseño revolt.