[>BKA< T Wrecks]

I don't think it's a big problem either way. There are basically 2 possibilities:
1) Leave those WPs out. Chances that a bot will fall down there are near to 0%, and chances that it will drop down from the ledge and fall into the waypointed area below are very high.
2) Leave them in, but unconnected. First leave the connection down, try to save your WP file. As soon as you don't get any errors, remove that connection. Save now, and you will be prompted with an error message. However, now you can be sure that it's the "error" you made on purpose and nothing else. Save, and you're ready. There'll be waypoints on the ledge (for the case of emergency), but no bot will go there normally.
One of these 2 (or both) ought to work on any map with a similar situation. I wouldn't know how to implement a kind of "damage calculation" or "emergency only" flag without giving up original PB waypoint compatibility.