The BaseApplicationPage and BaseUserControlPage files in your application’s ...\App_Code\Shared folder are replaced with new versions from the ProjectTemplates folder.
During migration, the existing BaseApplicationPage and BaseUserControlPage files in your application are replaced with new files. Any changes you have made to the BaseApplicationPage and BaseUserControlPage files will be lost during migration.
After migration, re-apply any customizations you may have made to the original files to the new files in your application.
Version 6.1 Application Migration