Hi
is that not more a question for the CAD community than for the Windchill's one ?
Anyway, there is no reason why you can't restructure your family table. However, this seems a complex exercice if instances are released and used in many assemblies.
I hope you have a test environment.
From my own experience Family Table were great when using CAD in Windows but using them in a PDM is a nightmare unless those tables once created will never be iterated. My users used to create Family table for all sort (eg sheetmetal where they could quickly turn on and off bending), this sounded OK when looking at the 2D drawing but when considering PDM and processes this was a real pain and I had to educate the users not to do that anymore.
Best of luck