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Generally it is not necessary to have the engine running whilst bleeding the brakes. In fact most mechanics don't even bother to bleed when changing pads or shoes. The risk of damage is very slight.
It is not unusual for the brake pedal to feel a bit spongy when new pads are fitted until they have bedded in. Just drive careful and increase your braking distance for the next 50 miles or so
Just a keep a close eye on the brake fluid level though.
Currently in madnoel10's garage:
Honda Civic 1.4l