Sorry I don't understand most of that.
There shouldn't be any feedback. Where is power being fed back from? Everything associated with the heating system should get its power in one way or another from the
'load' side of the same 3A fused spur, in a 'chain' of supply. So, the fused spur supplies power to the programmer, the programmer supplies power to the thermostat, the thermostat supplies power to the motorised valve, and finally at the end of the chain the motorised valve supplies power to the boiler and pump. So that only when the link is completed is power transferred down the chain programmer....thermostat....motorised valve....boiler / pump. There shouldn't be any thing connected that could cause feedback.
I would also be seriously worried that if I understand you correctly, you now have a heating system without a 3A fuse to protect its wiring and internal circuitry. If it's being supplied from the 32A MCB for the socket supply in the consumer unit, and as most of the heating system wiring / components will only be rated at a few amps what do you think might happen if a fault occurred?
Also, why a 3-Pole isolator? There's only one Live and Neutral supply for the whole heating system. Earth wires are permanent connections and not fed via switches. Below is how it should be connected. N L E from the load side of a 3A fused spur. You can have multiple wires in the FCU load terminals, but there shouldn't be any other mains supply into the heating components to cause any feedback.
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