2000 Honda Accord 2 litre 107000 miles.

I’ve just changed the front brake pads. Easy job (usually). However, this time I find that the pedal acts as though there is air in the system, yet the level in the master cylinder never went below minimum when I removed excess fluid. It feels solid with the engine off, but goes to the floor with it running.
In the past I’ve simply pushed the piston in with a G clamp, but some videos I’ve seen clamp the brake hose and release fluid through the bleed nipple. Should I have done that and why? Have I damaged any part of the braking system by pushing the fluid in reverse? Any ideas where I go from here? I tried bleeding them, but to no avail.