I struggled with the same problem but found a nice workaround. You cannot change whether it affects navigation at runtime, BUT you can set “Can Ever Affect Navigation” to true, and then use “Set Collision Response to Chnnel” for Pawn and Vehicle collision channels to ignore/block depending on if you want to rebuild the navigation or not. If you set them to block then NavMesh’ll dynamically rebuild the navigation, if you set them to ignore the NavMesh somehow won’t detect them and won’t rebuild the navigation. Hope it helps.