There is no need to reflash!
You just lost the MyDocs partition, which should, anyway, be deleted and later recreated smaller.
Just start the procedures of the linked howto http://wiki.maemo.org/Nitdroid_easy_install_on_EMMC again. First download the package containing fdisk : EDIT: Or go tuxsavvy's way and install busybox-power to get a working fdisk Through apt-get.
Right now your device has no partitions mounted to MyDocs, but the folder /home/user/MyDocs still exists.
Then follow the 'method2' procedure through to step 9. You then will have prepared a working MyDocs partition again and a seperate Nitdroid partition, aka. /dev/mmcblk0p5.

Good luck!