Well, you shouldn't delete the custom license field because it will effect customers that already have your app and if you app actually uses the license field. So the first change is to change the custom license field from "Required" to "Not required" (so edit the field and uncheck the "Required" box).
Next, in your application remove all references to getting and using that license field. So when new customers get your new version it won't use the field at all.
Then you should modify your scripts to not set that field any more.
Does that make sense?