This reminds me of one of my playthroughs in Divine Divinity. For some reason, all of the teleporters suddenly became deactivated, and I couldn't warp to any of them. Was quite an ordeal to finish that playthrough. Had to manually walk everywhere.
Do you have a save before the waypoints disappeared?
You could place a teleporter pyramid next to the respec mirror or on the top deck, so you can teleport to it. Not quite the same thing, but it helps.
Last edited by Try2Handing; 26/09/18 05:09 PM.