Team Fortress 2 - guide server.cfg

[ThermalSausage]

One of my friends owns/runs a TF2 server and would like to add custom maps and remove some of the valve maps that he doesn't like (Granary, CTF Well etc.). But for some reason the server isn't reading the map rotation file and the custom maps aren't appearing and the maps he removed aren't leaving. How can we fix this?

PS: I also have the RCON password so if there is any way of doing it through the RCON please let me know.