clear the library
Clearing the Library erases it and sets it back to the defaults. That's what it does. This includes any and all customizations you've made to your Media Views. So... I think you should explain yourself better...
All changes made to unlocked Media Views should persist when you close and re-open MC (locked views prompt you to save the changes when you navigate away from the View). There is an option to allow or disallow setting sort order permanently through List Header clicks, if you're referring only to sort order. And, there was a bug that caused the Tag Action Window's Show Tags in Current View mode to not work correctly with recent builds. If this is what you mean,
this can be fixed. One important thing to understand, however, is that Client copies of MC cannot make changes to any Media Views on the Server. MC does allow you to make the changes on the Clients, but all changes made from a client are lost when the client is closed and re-opened (the Server's copy of the Library always wins). Clients can make changes to File tags, and they can create and modify Playlists. They cannot change any Media Views, or change the Theater View setup.