If you flash the eMMC image yes, you could also use the MeeGo initrd image, then press U and export the eMMC over USB, then you can use any partition manager like gparted to restore partitions.

Not sure if it's documented anywhere, but here's the page for the initrd, it's quite simple to do and doesn't require you to flash the device's eMMC or rootfs, just make sure you have a full battery before doing it. http://wiki.meego.com/ARM/N900/Using_Rescue_Initrd

And before you ask, no, it does not alter the rootfs or the kernel, it runs from RAM.