The BaseApplication files in the \App_Code\Shared\ folder are replaced by new versions from the ProjectTemplates folder.
During migration, these BaseApplication files are replaced with new versions:
…\App_Code\Shared\BaseApplicationMenuControl.cs (vb)
…\App_Code\Shared\BaseApplicationPage.cs (vb)
…\App_Code\Shared\BaseApplicationRecordControl.cs (vb)
…\App_Code\Shared\BaseApplicationTableControl.cs (vb)
…\App_Code\Shared\BaseApplicationUserControl.cs (vb)
Customizations you have made to these files will not be retained. If you have customized these files, then you must re-apply your customizations to the new files.
After migration, re-apply any customizations you may have made to the original BaseApplication files to the new BaseApplication files in your application.
Version 6.0 Application Migration