It's not a problem, GSX CAN handle multiple .INI files, they will be named automatically XXXX1.INI, XXXX2.INI ( xxxx would be the ICAO code) and it will automatically use the one with the matching AFCAD name.
So, in your case, you could do the following:
- Do the whole customization using the same AFCAD
- Switch to another AFCAD
- Customize ONLY 1 parking, enough for GSX to create a new .INI file
- Copy&Paste all the parking sections from the first .INI to the new one using a text editor. Just the parking section, leave the [general] section as it were, because it contains the name of the AFCAD in use.