@stem Presumably the brown that was disconnected was the live feed to the grey on the 2 port valves, so by disconnecting that the boiler wouldn't get a feed when the valve opened.
It's a possibility that the 2 port valve microswitches also pick up their live suplies from the thermostat connection, but they could also get then from elsewhere. However, that was what I was thinking when I said it would be worth checking the hot water function again. However, it is irrelevant now if jinglieD goes for another programmable thermostat upstairs, as the programmer wiring will remain as is.