Each controlled site has two backup methods of controlling the signalling: The ELCP (Emergency Local Control Panel) which can be operated by a member of Operating Staff, or the Maintainers panel/terminal, which can only be operated by the maintainer.
However each takes time to put in (and needs sufficient qualified staff) and in the event it is often faster to stop all train movement and go for a reboot of the control computer.
In the old days (pre-ATP/ATO) trains did run on just red and green, however now all trains running on the line have to be ATP fitted. Anything running without ATP (i.e. in restricted manual) have to treat a white aspect as a danger aspect.