I split your post into a separate thread because the forum guidelines tell you not to extend old posts (especially when your post is only loosely related to the original one, and it was a very old thread).
Anyway, if the "backgate" is controlled via a pcell parameter, then yes you can remove the backgate by altering the parameter on the instance using SKILL. Otherwise you could write SKILL code to flatten the pcell and search for the shapes and delete them. Or you could write your own pcell with the same parameters, and then have a pcell which instantiates the original pcell, flattens it, and then deletes the shapes you no longer want.
Your question is rather lacking in details; it is rather dependent upon the facilities provided by the pcell you're talking about. As a result I'm having to give general answers, and can't say which would be the best approach in your case.