The only way waypoints can be removed from the unit waypoint library is with a manual "Format Nav Directories" command under the Setup tab ...

Or deleting them manually thru the waypoint management menu under the NAV tab ...
-------

It would be a good idea to export your new waypoints to a SD Card and import them into HBPC ... Then also import the waypoints from your old unit into HBPC ...

Then you can easily edit the waypoint names to make sure you don't have any duplicate waypoint names ...

Rickie