If you are willing to use something outside of LaunchBox, you can use something like Notepad++ under the "Find in files" tab to mass edit by replacing all the directory references in the XML files. Make sure LaunchBox is not running if you do this.
The app isn't supposed to do that. I will have to do some testing here to see what is going on. The app hasn't changed in a very long time. No one else has mentioned the symptoms, but doesn't mean much in the real world. Thanks for bringing this to my attention. I will report back.
The app does not turn that option off, per sec, but it does copy the default retroarch.cfg file, so if you haven't turned that option on and saved that in your default settings, you will see that behavior.
Really not sure then. I switched cores to Gearcoleco and renamed the bios rom file and Retroarch runs all my Coleco games with no issue. Just for info, I'm running Retroarch 1.16 and Gearcoleco 1.0.1.