Running fastboot -w update softwareupdate.zip with the -w flag you are overwritting the recovery and boot flashed on the previous steps PLUS deleting all your userdata from the phone. ALL.
$ fastboot help ... -w Erase userdata and cache (and format if supported by partition type).
I really hope you made a backup of important stuff from TWRP before executing the third step you describe. That was the only purpose of my tutorial.