Is there a Way to Mass Delete an Affiliation Code only from some Profiles?

No, unfortunately there is no tool to mass remove the affiliation code from only certain profiles. You will have to manually remove the affiliation code from those profiles that do not need it.

Optionally, you could do the steps to remove it from all profiles and then add it back to only those profiles that needed it. Here is how you would do that below. It is recommended to copy live to demo and do these steps in demo first and review the results:
 

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. Click Yes on the confirmation pop up – you will receive confirmation that a certain number of profiles had the specified affiliation code removed.
5. Go back to Profile File Maintenance >  Profile Code Maintenance > Affiliation, find the code, double-click to open, and then un-check the Temporary box in order to be able to use it again.
6. Create a text file in Notepad with the ID codes of all profiles that need the specified affiliation code. This file could be created from an export out of FIMS in which you perhaps created a custom data grid or user defined export to identify all of those profiles that need the specified affiliation code. Header would be ID code and then each line would list the ID code of a profile, for example: