I have a conventional gas central heating system.
There are 3 zones including hot water. When I switch on the main heating for the house the boiler fires up for a few minutes and then the pilot light goes out.
If I turn off the house heating and just require hot water, or for zone 3, the boiler works properly cutting in and out with the pilot light staying on.
I can only assume that the pump is stating to fail and cannot pump the hot water around the radiators and so the boiler is over heating or that the central heating pipework is partly blocked causing the boiler to over heat.
Forgive me, but I wouldn't draw that conclusion at all.
If the pilot light is being extinguished, then there is a fault within the boiler. It could be a faulty thermocouple or incorrect burner setting for example.
I would be dubious of the link you are making between hot water only and heating. I suspect that might be simply a coincidence or the fault is more likely to occur possibly because the burner is running more often and for longer when the heating is on.
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