Were the kegs disconnected from the gas for a few days or more during the swap to the new kegerator? If so, and there was a leak, they could have lost their carbonation. Differences in the serving line don't change the carbonation level in the beer. They can cause you to lose carbonation in the form of foam if they're too short for the pressure and temp, but that's about it. Sounds to me like your beer lost whatever carbonation it had somehow. What pressure are you serving at? At a warmer temp like 41° your initial thought that 3' lines are too short is correct. You'll likely need 10' or more once the beer regains it's carbonation.
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