we all know here what rootFS-only flash does, just like we certainly know what flashing with EMMC.bin does...
the OP's situation probably needs complete flash, so the new FW can be properly reinstated. As he was apparently aware of concept of flashing in his post already, he'd certainly realize there could be a situation of losing data...that's why the BACKUPS exist...flashing the phone with EMMC.bin is no heart-breaker, as you outlined...it's simply the best way to reinstate the FW into a out-of-factory state and helps getting rid of most issues with N9, and yes, WITH losing all personal data...
nevertheless, nobody asked you to be offensive...