Sounds completely OT in this thread but what the heck...

This is my understanding:

• The "combined" image flashes the NAND, It is called "combined" because it "combines" some (all?) of the NAND partitions into a single image. It flashes the kernel and the rootfs. (Anything else?)
• Un-optified apps are installed in rootfs. Therefore, flashing the "combined" image will wipe them. Moreover, some apps store their data in rootfs as well. Notably Hildon Desktop (/usr/share/applications/hildon). Flashing rootfs will wipe that too.
• Optified apps that store their data in rootfs (a few naughty ones) will survive but the data will not. Sometimes just running the affected app will recreate default settings. That means that e.g. a Foo game will work but your saved levels and top score table will be reset.
• Optified apps that store their data in /home (most of them) will survive. So the Foo game will remember the saved levels and scores.
• Here's a twist though. Optified app themselves may have survived but, since both /usr/share/applications/hildon and /var/lib/dpkg are on rootfs and have been reset in the flashing process, their menu entries, as well as any record of them ever being installed in the first place, will have gone! In other words, you get crippled apps. The only way to get them back is to reinstall them.