Yes you can damage the seals on the piston by travel beyond the normal range of movement in the bore, but the damage is caused by rough/jagged corrosion in unused portion of bore, and if your MC is virtually new, that's far less likely to happen. Travel beyond the normal range of movement would only occur if there was say a serious hydraulic leak somewhere, or if during two-man brake bleeding (how did you bleed your system?), the pedal was pushed beyond its normal range.
With the engine off, does the pedal creep down all the way if you keep pressure on it? This would be typical of a bad MC. If the pedal creeps down with engine running, then this could be normal behaviour. With engine off, does the pedal harden up with a few pumps?
Were the brakes working ok in past with the new MC? When did the problem with the brakes start, and what was the last work you did on the system before this? You mention replacing all the pipes - did this include all the flexible hoses?
The most likely problem is that in replacing all the pipes you introduced a lot of air into system, and some of this air is 'hiding' at points in system higher than the caliper bleed screws. If there is a brake line junction high up at rear (this is the case on my 928, but I don't know if 944 has similar design), then the solution is to actually unbolt the calipers, and hold them higher than that junction while bleeding system to encourage air to move towards bleeders. It's also possible to have air hide in the ABS pump.
_________________ 928 S4 Amazon Green 91MY
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