As a member of the giffgaff network, every time I get new firmware (in my case via Odin) the giffgaff APN's have to be reinstalled.
When using gingerbread, this was not a problem as the app APN Backup & Restore did the job in a click.
With ICS and Jelly Bean this option has been blocked for security reasons, and so it's a manual operation, and requires the giffgaff settings.

Well I've found a solution, and it's using good old APN Backup & Restore.
The instructions are on the Play Store site, but basically you have to have a rooted phone and Titanium backup installed.
The APN Backup & Restore app is converted to a System App using Titanium backup (it's just a click). Now it can be used as before to delete/backup/restore APN's.

Can confirm that it works on the Galaxy S3.

APN Backup & Restore here: