It somewhat depends on which part of the eMMC you are talking about. If it's the 27 gig partition, then probably the easiest way is to connect your phone in mass storage mode to a windows machine and run the check disk thing over it. (Or if you have Linux you could use fsck.vfat / dosfsck - or just use the same tools on the n900 itself, though unmount /dev/mmcblk0p1 first)

If it's the 2 gig partition I'd be inclined to run android (or ubuntu or something) from the external memory card so it can be unmounted, then use the same tools to check it.