If you make a backup of the phone, such as with ClockworkMod Recovery, it can be used to "restore" the phone to a freshly formatted SD card. I just had to do that when my SD card became corrupt. After formatting the card with ClockworkMod Recovery, I hooked the phone up to a Linux PC and copied all my files I had burned to a disc back to the card. That also copied back the backups I had made with Clockwork. Then I booted ClockworkMod Recovery and restored one of the backups. I presume Titanium Backup would also do the same things.
So I would think you could also do it to a new SD card, once it is formatted for the rooted environment (an EXT partition of 512MB on the card). I'll find out Wednesday, when my new, larger, card gets here and I have to try this procedure again.
Zoandroid