FF6Tools - Browser-Based ROM Editor

I restarted from scratch because there was issues with event triggers on previously edited ROMs as expected of the changes you made. I changed straight away the NPC in Ghost Train (NPC located at 16, 8 in map 145) by just moving the NPC elsewhere on the map and when saved, he started to appear in the other wagon again.

From what I can see in the event viewer, the event triggers disable all NPCs that have the NPC 521 switch so it does remove most of them as expected, the seller NPC has the 615 switch so I thought that was the reason why it didn't get removed.  If I change the switch of the seller NPC to Switch 521, it either disappear completely in both maps or changes into an NPC that says "look out!" that provoke an encounter (I can't say which one of the 2 it really is for now).

I have to admit, before now I hadn't looked closely enough at the phantom train interior maps to realize how they work. I tried to replicate this issue but I'm not sure I quite understand what the problem is. Here's what I did:

1. Open a vanilla ROM with FF6Tools
   
2. Go to map 145
   
3. Select the ghost at (16,8) and move him to a different spot on the map (this is the ghost who sells stuff)
   
4. Run the ROM in an emulator and look for said ghost (I found him in all 3 train cars)
   
5. Run a vanilla ROM in an emulator and look for said ghost (again, I found him in all 3 train cars)
   

Are you saying he's not supposed to appear in all three train cars? Which ones is he supposed to appear in?

Starting from the right side of the train (and ignoring the caboose), I counted 5 ghosts in the first car, 4 ghosts in the second car, and 6 ghosts in the third car (not counting the one who shows up to block the door). I get the same count in both the modified version and the vanilla version. I believe NPC switches 518, 519, and 521 control which ghosts are visible in each of the first three cars, respectively. So if you want a ghost to appear in only the first car, set him to NPC switch 518.

Like you mentioned, the ghost who sells stuff is NPC switch 615. I dug through the event script, and the only reference to NPC switch 615 is when it gets turned on when you board the train (see CA/AA93). So as far as I can tell, that ghost should always be visible.

One thing I should note, if there is more than one trigger on the same tile, you can cycle through them by clicking on that tile repeatedly. I noticed that there are actually 3 different ghosts at (12,8). You might have realized this already.

I also checked map 151. I made one of the ghosts sell stuff, and he only appeared in one train car. At (8,10) there are actually 2 different ghosts on the same tile which show up on the two different cars. One of them joins your party and the other is a battle. Again, NPC switch 518 is for the first car you enter and NPC switch 519 is for the second car.

I hope that clarifies things a bit. Let me know if there's something specific you're looking to accomplish and I can try to help more. While testing, it might be helpful to change graphics/palette/etc to make a specific ghost easier to identify.