If it works the same way as my 800 you can remove the individual trip files the totals are stored in a separate file.
Individual trip files \Garmin\Activities\2013-XX...........XX.fit
Total data \Garmin\Totals\total.fit
I transfer my .fit file to http://ridewithgps.com/ then delete them, and use the web site to track my totals, but I just checked on the GPS and my total is still there, but I know if you delete total.fit file its back to zero (had to do a hard reset once).
On the Garmin 500 deleting the individual rides does not delete the totals. there is an option on the garmin to delete individual rides, but it is far easier to browse to the folder through a PC USB connection.