Question for phones with inbuilt flash storage

Ok, so I learned from Samsung today that I can get the Gingerbread update via manual flashing from the Samsung Service Center in a mall here. Now I am wondering, since AFAIK an update will wipe everything on the phone, but the SD card would be untouched. Would this be the same for phones with inbuilt storage? My phone has 1.5gb storage which is read as an SD card by apps, instead of reading the external SD card. I was hoping to be able to keep this safe, so I can move my apps from my phone memory for apps to this memory so that their save states would not be wiped.

EDIT:
I just realized, 1-click root is available for Galaxy SL. I've never rooted my phone yet, but I think I can just root, back-up, unroot, take to service and then root and restore. Would that be feasible?

 

I said, the sd card is in built storage space, apps that back up to sd card dont read the external sd card as an sd card directory, and they read the inbuilt sd card. its like the N8 for example, you have phone memory, then you have mass memory. Its not like I can remove it like a normal sd card when i have the phone flashed.

My phone storage is

Internal phone storage: 1.87gb - for apps
Personal data: 72.27mb
Internal SD card: 1.52gb - basically just extra memory used like an SD card but is inbuilt
external sd card: 8gb

Basically, my phone has 2 sd cards, an internal one and an external one. I cant move apps to external sd, at least apps I've tried like App 2 SD dont support that AFAIK. back up to PC? back ups to PC only back up contacts and calendar etc, which I dont really care about as I am using cloud sync for those.