Set User Flag if Waypoint Added/Updated (File>Load GPX/LOC)
Click this check box if you want GSAK to set the user flag for any waypoint that is added or updated in the database. This is a useful way to determine which waypoints were updated or not.
If all you want to do is know which waypoints already exists in the current database, then also check the "AND only update user flag if matched". When you check this box, then only the user flag is updated - no other information is overridden (Unless of course if the waypoint did not exist in the first place, then it will be added to the database with all the information and the user flagged checked).
If you do not want waypoints added to the database, then make sure you also select the "Existing Only" in the "Database Options"
Finally, if you are updating the user flag, you can make sure all user flags are cleared in the database before loading the GPX files. Just check the "Clear all user flags first" box. You would usually do then when you want to make sure that the ONLY waypoints that have the user flag set are those that meet your criteria for this load.