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I've never heard a ST9400A programmer make any beeping noise, and it's backup battery isn't replaceable. The same applies to the ST9100C timer.Are you certain that the beep isn't from a smoke alarm?
I've heard smoke alarms make a beep that is so quiet it's almost inaudible. Personally, I would unmount the smoke alarm and wrap it in a coat or blanket, and see if you can still hear the beep at the same level.It sounds like you have a Honeywell room thermostat, in which case it's not overriding the programmer. The room thermostat actually switches on the heating, indirectly, when the room temperature drops, and switches it off when the temperature reaches the setting on the thermostat.
Hello, did you find the source of the beeping?Do you have a CO alarm?