The semaphore signals were train order signals. They indicated if an approaching train had train orders waiting for them. Such orders might change previous instructions the train would have received regarding changing the meeting point with another train, or other important items. A train order signal as an "absolute" signal, if it was set to red, you stopped.
After the agency was closed in the early 1950's and the depot torn down, the signal was moved to section house, in case a temporary agency was ever needed to be established at Cumbres. To my knowledge, no temporary agency was every enacted at Cumbres, and the train order signal was never used after it was moved to the section house.