I actually keep a backup of the original game on a separate drive and then also another folder with copies of all the mods.
You'll find that, over time, there will be a ton of similar mods out there by different makers and maybe you can't decide between some (like CFs, courts, etc) or you may want to go back and forth between some (like with overlays- ESPN or TNT, for example) or realize you want to backtrack on some others (like with all the different globals-I think I have damn near every shadowmod from 2K11 on file).
Often you can still find older or different versions online, but sometimes you can't and it's easier to keep them on tap for quick access anyway.