There is a way to mass delete the code from any Profile that has it. 

Follow these steps to mass delete the code from Profiles so you can remove the code from the code table:
  1. Go to File Maintenance > Profile Code Maintenance > Affiliation, find the code, double-click to open, and check the Temporary box. 
  2. Save and close.
  3. Then go to Profile File Maintenance > Delete Temp Affiliation Codes and pick the code you want to mass delete from all Profiles that have it. If you are using Affiliation Code Grouping and you want to delete all the system-generated Group codes associated with that code, check the box that says Delete System Added Group Affiliation Codes.
  4. Then go to File Maintenance > Profile Code Maintenance > Affiliation, find the Affiliation code, double-click to open, and click the X on the toolbar to delete it.