You can replace product categories that are used within the app by updating the iFrame URL and Mobile iFrame URL fields in Magento.
To do this go to System>Configuration>General and expand the G3D Personalise-iT Product Selector Settings. Within each of the fields you will see a link that controls the app on the site.
Within the link you should see the parameter &pc= followed by some 5 digit numbers that are separated by commas. You just need to replace the old category ID with the new one there to make the change.
The change may take upto 24 hours to come through to the front end if you are running the app from the CDN.