this may be related to filesystem used on the sdcard. i read (even i don't remember where), if i remember well that if there is no vfat partition or if you configured a special partition scheme. The update may reset to defautl config and n900 would not be able to read your table partiton of the sd card. or somthing like that.

Solution was to modify your partition entries in the related boot file to set to your sd card one.