Hello AJ Fariss !

Yes, enabled the "Force auto-update, even if some files were modified" parameter may solve your trouble, but yes, it will erase your custom code things, which you made in the files of the core and default UNA modules. So in this case you need to keep all changed files on PC, made auto-upgrade and apply these changes back. But if you have done all your changes via Studio then nothing to worry about it (but it useful to backup your database and files before such procedures).