Here is one example that will force a reflash of the N800 with the latest OS installed.
The repository http://repository.maemo.org/pool/bora/free/binary/ has the libgtk2.0-0_2.6.10-2.osso30_armel.deb package that contains a broken gtk-x11 lib. So if your sources.list references the above repository your next reboot after your procedure will hang at ~90% (the splash screen with the Nokia hands will not show up) and cycle rebooting.
There are people here on the forum who claim this is expected behaviour.
http://www.internettablettalk.com/forums/showthread.php?t=8992