I want to change all 3 column layouts to two columns. So am I to change the master page embed of every file from ThreeColumn.master to TwoColumn.master?

MasterPageFile="~/MasterPages/TwoCoulmn.master

If I do that then when there is an update will all of these changes be reset?

I sure wish theming was independent from the core files. Sure we can adjust the CSS in App_Themes but layouts are called in through nested master pages from all of the .aspx pages.

If I save my changes then will I need to apply them to every future version again?