Even if just kernel reflash doesn't work, reflashing the fiasco image as a whole should be fine. No need to reflash eMMC. That's only for really bad cases.

As an example, I ran fsck on my /home partition, while it was mounted, like 3 times. Partition was massively screwed, and phone would barely boot past the Nokia screen after that, then reboot loop. Merely reflashing the fiasco image fixed it, and there was no need to touch eMMC. (I reflashed both, eMMC included, shortly there after, for other reasons, but it worked well enough for me to get everything I needed off my eMMC MyDocs storage without a single hitch.) Since the /and directory is presumably within the N900's rootfs partition, a fiasco reflash should definitely be sufficient (though merely kernel reflash may not be).