I created "Test Folder" and then put "List 1" and List 2" in "Test Folder"
Then I added Waypoints A, B and C to "List 1" and Waypoint A to "List 2"
I have the map in the lower left corner and the listing of tracks and waypoints in the main screen.
If I click either "Test Folder" or "List 1" Waypoints A, B and C are listed as expected.
If I click "List 2" then only Waypoint A shows, again as expected.
Then I removed waypoint A from "List 2".
As expected, "List 2" now shows no waypoints, and List 1 still shows A, B and C.
However if I click "Test Folder", only A and B show. Waypoint C is missing. This appears to be a bug.
If I close Basecamp and then restart, clicking "Test Folder" shows A, B and C, which is correct. Therefore it appears that closing and restarting Basecamp is necessary to refresh the waypoint count properly after removing a waypoint from a sub-list.