Okay.
Its possible that something went wrong during the scenery installation and, unfortunately, it probably can't be undone - at least not easily. The only simple way to "delete" an AFCAD file is to overwrite it, which won't help in your situation.
What I will advise you to do is create a new file to use in FS2002.
Go into AFCAD and open the KMCO file(s). Pick one that you would like to use for FS2002 and export it to the fs2002/Afcad directory (go to "File" and click on "Export Airport.") This converts the file to .txt format so that it can be edited. Close AFCAD.
In Windows Explorer, go to that directory (C:/Program Files/Microsoft Games/fs2002/Afcad) and open the file you exported in notepad. Near the beginning, you will see an entry for the "ICAO Symbol." Change this from KMCO to something else that will make this facility easy to identify in fs2002, such as "2MCO." Then go to the end of the file and find the entry for "Airport Name." Again, change this to something easy to distinguish, but different than what has been used. I'll suggest "Orlando Int'l Active." Save the changes and close the file.
Open AFCAD, click on "File," select "Import Airport." If you changed the ICAO symbol to "2MCO," then you will select the file by that name. The file will display in AFCAD as you saw it before. Save the new airport. You will get a prompt asking if you want to add this airport to airports listed in the city of Orlando. Choose "yes" and close AFCAD.
Open FS2002, go to "Create A Flight," and the new airport should show up on the list under its new ICAO symbol and name. This will be the airport you use in fs2002.
To get AI traffic to fly to the new airport, the flight plans will have to be edited. If you have Traffic Tools, this will be easy to do. Before you edit, you will probably have to create a new entry in the Airports.txt file for the new airport.
Good luck!!

Erik