The route is selected based on the last known route status identifying the safest path of the shortest distance offering the quickest resupply to the unit gaining supplies. If the last route used was interdicted to the point where supplies and vehicles are lost, it would be dropped as an option for planning the next supply pulse.
If the player clears an interdicting unit from a different route, then it becomes the safest option for the planning and delivery cycle. If two separate routes are cleared before the next supply delivery, then calculations focus on finding the best among those routes and any previous route which was not interdicted during the last pulse.
Interdiction locations could be reported by radio, or from debriefing the units which escape damage and return to base. If 100-percent of a column is lost and there were no radio, you're right, the location could only be identified by observation from units not involved in the combat.