I was helped through this by a superb VMware Storage group tech.
His blog is here http://www.virtuallypeculiar.com/search/label/VDP
After you change the FQDN using the configuration tab in the VDP appliance configuration portal,
https://your-VDP-applance-FQDN:8543/vdp-configure/
backups and full level restores work, but File Level Restore (FLR) is broken.
You must manually change a setting in the
axionfs.cmd file located under /usr/local/avamar/var in the VDP appliance.
you must change the server line in the file to reflect the new FQDN.
--server=new-FQDN
FLR will then work.
The bottom of the configuration tab may still show the FQDN of the old internal proxy, but this does not matter.
File Level Restore will work.
I can only confirm that this works for the current version of VDP
v6.1.4.30