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Intermittent faults are very challenging to fault find.
If you turned on the hot tap when the fault is present does the boiler attempt to start (can you hear the van starting for example) and does it show any error codes?
To my mind this type of fault would be down to a faulty relay on the control board, if you have already replaced the flow sensor its clearly not acting on the input for demand of hot water.
The fact the fan starts suggests the PCB is detecting input from the flow sensor, but then not invoking the ignition sequence.
Taking into account the boilers starts first time for CH and your not getting a fault \ lock out codes rules out other sensors and electrodes, and would be confident that the fault lies with the PCB.
A new PCB costs around £150, you would need a gas safe engineer to attend to replace the part, however based on the cost of the part I would be inclined to go for a fixed price repair and protect plan, SSE do one see the bottom of the page here.
Should you prefer me to recommend a local engineer please provide you postcode.