Go to Help > Open Settings Folder and copy the file PluginPresentation.settings and paste it somewhere safe to save a backup of that configuration.
If it ever gets cleared out when or if settings are ever refreshed or corrupted...
1. Go to Help > Open Settings Folder
2. Be sure to quit Studio One. (this is important as it writes these files on quit)
3. Copy the PluginPresentation.settings file from your backup and paste it into the settings folder, overwriting the one there.
Now when you start Studio One again all of your custom browser folder arrangements should come back.