Previously we did not differentiate between non-player characters and player characters in the respawning/checkpoint logic. Now we do. Player characters (possessable) will use checkpoint but NPCs will not. NPCs always respawn at their default positions if killed.
This may have some knock-ons, of course. In the example we are giving the player character has 6 controller sensors all of which are set to "remote control". No controller sensor was possessed and so the character was not treated as player character. Instead it was treated as an NPC and respawned at the start of the level.
To fix Prometheus we simply set the main controller sensor to possessable and force possession, the character is now treated as a Player character and can make use of checkpoints.