I have the same problem, I modified the EMMC to 3 GIGAS a year ago. since that time I have never been able to flash the EMMC, I can only do it in rootfs without problems. I have used all the commands in maemo flasher as you say over and over again, without using the-R and repeating the steps but no case, only sometimes successfully flashing rootfs. Before my mind could enter mydocs without problems, but when trying to fix mounting and dismounting, to fsck from the terminal I found this reading in all forums to understand and be able to run different command that you know how to use ... but it got worse, now my EMMC (OPT) is corrupt, and I can not delete some folders that are broken. Now I can not enter MyDocs, says "memory card corrupted". When you restart the N900 throws the message "device storage format unsupported" but the rest of the phone works. When connected via USB as mass storage works. MyDocs memory appears and I can use it without problems from your computer.
from terminal:

/home/user # mount /home/user/MyDocs
mount: mounting /dev/mmcblk0p1 on /home/user/MyDocs failed: Stale NFS file handle
Urgent need to restore factory settings. Is that possible? Please help me. I'm sure many have this problem and still fail to flash the EMMC.