Waypoints and software version are different...

The software is more like an update to the "operating system software"... Whereas the waypoints are stored in memory...

Export the waypoint Nav data to a blank formatted SD card...(you are exporting a "copy" of the waypoint data...the original waypoint data will still be on the unit)
Delete the Nav Data from the unit....

Follow these instructions for updating the software in your unit...(use a separate blank formatted SD card)
How do I download Software to my HB Unit using MMC/SD card?

After completing the update process from above...
Reinsert the SD card that contains your waypoints...

The Unit will automatically reinstall the waypoints from the SD card...

The unit should recognise that the Nav data has been imported (into the unit memory)...

Remove the SD card that contains the "copy" of your waypoint data....(save this SD card with the "copy" of your waypoints for a backup in case something happens in the unit to lose or mess up the waypoints in the unit memory)..

Rickie