Unspoiled Nodes have their own rules. BUT, for the rest of them :
There are FOUR sets. They are either all regular nodes (single or pair), OR one set is the Ephemeral node.
Touching (moving to and accessing, doing anything else not required) the third set causes the first set to respawn. This is why you can go to an Ephemeral node, and to get it to repopulate, simply run and touch two of the other three nodes in the area, and touching the Ephemeral gets the first other one you touched to repop.
