Hi, from what it says on the maemo wiki page (wiki.maemo.org/Updating_the_firmware) I just go with this :
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.

I don't flash the eMMC so i keep all my contacts, conversations etc. when reflashing