Yes the procedure is same. Do it when system booted from flash. There is no need to delete previous system from mmc (if you use 'rsync -avH --delete source/ destination/') but it won't hurt.

In fact it may be a good idea to format second mmc partition again (mke2fs /dev/mmcblk0p2) like said in the beginning of instructions (part 2 of https://maemo.org/maemowiki/HowTo_BootRootFSFromMMC ) . Especially if system on mmc previously crashed few times and was not repaired by e2fsck.