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If you are not already commited to a large set of decoders, you could consider installing models which support braking when they detect an asymmetric DCC signal. This is called "ABC" by its inventors - Lenz, and is supported by ESU, Zimo and a few others as well. When you want a locomotive to stop automatically in a particular section, you switch on the asymmetric signal, the decoder detects it and comes to a halt within the distance programmed into a CV in the decoder. How you switch on the asymmetric signal is up to you, but you could use a set of contacts from the points.
David
David