Buildings placed within the range of a spyglass will not get upgraded to stone by the masonry building. Once the spyglass is removed and the buildings are removed and replaced, they get upgraded immediately.

Game version 1.004.000

Clip here: https://1drv.ms/v/s!AjhW85e2w4crhL8aA4zWuPmSdVlH0A

As the clip shows, removing and replacing the tower does nothing until the spyglass is removed.