I know very little about Navaids in general so this might not be much help. AFCAD includes detailed instructions which explain things much better than anyone can do here. I suggest you read section 5. What you Cannot Do With AFCAD. This refers to the FS2002 version of AFCAD.
Visual elements
You cannot use AFCAD to change the visual location of runways taxiways, buildings or other objects at an airport.
NAVAIDs
AFCAD can display the location and other information (identifiers, frequencies etc.) for NAVAIDs, And you can change this information, but it does not change the actual NAVAID signals that your aircraft instruments use, it just changes how the NAVAIDs are presented on Flight Simulator map views and the GPS window. The NAVAID information that your virtual aircraft instruments actually use comes from a different set of files that AFCAD does not work with. It is interesting though, to see where the NAVAIDs are actually located at an airport, and you can often see some glaring errors in localiser and glide path siting.
SOME OF MY AIRPORT'S RUNWAYS HAVE BEEN A LITTLE OFF SINCE I DOWNLOADED SOME NEW NAVAIDS FROM FS2004 WEBSITE. I GUESS THEY WERE NOT COMPATIBLE. I DIDN'T BACK UP THE OLD ONES SO HOW CAN I REVERSE THIS WITHOUT HAVING TO RESORT BACK TO MY FS2002 CD?
The FS2002 & FS2004 AFCAD files are completely different. FS2004 updates will not be compatible with FS2002. It will depend how you installed these updates. Removing them might be a simple matter of deleting the BGL files from the Addon Scenery\scenery folder. If you activated them via the Scenery Library delete the new area from there first before removing them.