I followed this wiki

https://wiki.maemo.org/Updating_the_firmware

I used flasher-3.5 for XP

I have a retail version of the device and noted this paragraph.

Flasing the eMMC resets the MyDocs folder contents to factory settings. N900 users don't need to reflash the eMMC of their device. If you are reading this it's probably because you got a pre-production device e.g. in the Maemo Summit. If you have a sales unit and you have problems with your eMMC you should contact Nokia Care.