I'm making a quest and am not interested in building a whole new cave for it, so I duplicated Greywater Grotto (right clicked on it in Cell View and hit "Duplicate"). I put an entrance in the wilderness, linked the load doors, created a new Encounter Zone, and Edited all of the data in the Cell window, at least to the point where the cave works as it should for the Player in game. I can travel in and out of the cave and it says "To MyNewCaveName" as I approach it from outside.

My quest requires an Actor to enter the cave. I have set up a travel package in his alias and the target is an XMarkerHeading in my new cave. I have even edited the XMarkerHeading so that the Encounter Zone is set to my new cell.

The problem is, when the quest gets to the appropriate stage and the Travel Package kicks in, my actor runs to Greywater Grotto and enters that cave. Then he disappears completely from the game (as far as I could tell, he was neither in Greywater Grotto nor MyNewCave). I checked to see if I accidentally linked Greywater Grotto to MyNewCave interior, or if I accidentally placed the XMarkerHeading in the wrong cell, but neither is the case.

Does anyone have any idea about what I need to change in order to get him to enter the correct cave? Thanks in advance.

Could be a navmesh issue. Did you finalise the navmesh on both sides of any doorways?