Newer versions of Garmin POI Loader (v 2.4.0 or higher) have an option to uninstall all custom POI's from your GPS.
After selecting your GPS device, look for this option on the page that follows:
Remove all previously installed custom POI's from your device
Using this feature does not remove the regular built-in POIs that were pre-installed on your GPS.
Note: For units that come preloaded with the the NTTS trucking database, it appears that POI Loader DOES delete this information. Like custom POI's, it is stored in a gpi file.