What specifically do you meant that you "change menus.xml and DWMainWindow.xml in my extension file"?
You should not be changing those files, you should be using the MXI tags to add menu items. When you uninstall your extension Extension Manager will remove the added menu items. based on "when i disable my extension it delete DWMainWindow.xml" It seems like you include that file in your MXI, you should not do that! Never ever overwrite any built in Dreamweaver file, otherwise you're bound to run into issue like it seems like you're seeing.
Look on page 26 of the MXI format to see the menu-insert tag and into the next couple of pages to see some sample code for adding menu items: