I didn't flash the eMMC - though the wiki isn''t very clear on why one may need to:
http://wiki.maemo.org/Updating_the_t...MC_in_the_N900
Though it does specifically mention pre-production versions of the N900.
Flashing the eMMC resets the MyDocs folder, will delete all your personal data - music, documents, videos, etc.

P.S. one thing I forgot to mention, flashing will also delete your email settings.