You should be able to do any of your modifications without adding any new pipe network. I changed pipes and structure to different alignments all of the time without issue keeping it all on the same pipe network.
The news is not all good though. There is a serious flaw in Civil 3d calculating pipe lengths ans slopes when you are using rectangular structures and especially if you are using these calculated numbers for your drainage calcs. Civil 3D resists using wall to wall design methods and even though there are ways to force things to look correct, the numbers between structures is always off depending on the slopes and deflections off perpendicular of the pipe runs. Even an absolute 90 degree deflection at minimum slope will yield a pipe length 0.01 high. I also believe all crossing calculations are based upon the assumption the pipe runs from center/structure to center/structure and the cheats necessary to get good lengths and slopes will bust the crossing calcs. If you are able to design to structure centers most of these problems will not be an issue but if you must do wall to wall design, I suggest a field trip to the ship yards to expand your vocabulary of expletives.