Hey,
I used an older version of adventure creator to make this game:
The Armoire My nav system was a lot of walk to this marker, fade out, swap nav mesh, then teleport to new playerstart, I'd swap cameras fade in.
So I'm trying to do the same thing here with a new game I'm working on. Here's an image of my scene:

I've tried about every combination of those actions. Even disabled player movement, threwin a wait, threw in a pause, told it to also walk to the new player start.
No matter what the character falls back into the old nav mesh where it was told to walk somewhere. It's very frustrating...
I need this to have a 2d game where I can change scenes without literally have to duplicate every character, turning them off, then turning on character and swapping main character a bunch << the most hackiest solution. T_T
Some one help me.
Comments
What versions of AC and Unity are you using? It's not clear from your description if this is because the player is not recognising the change in NavMesh, or if it's because their intended destination is still on the old one. We will need to see the exact Actions and steps you're taking in order to properly help.
Be aware, however, that in AC v1.54 you can now have multiple isolated NavMeshes active at once by attaching PolygonCollider2D components as child objects of your main NavMesh.
When you refer to disabling player movement, are you talking about the Movement method in the Settings Manager, or the Movement system in the Engine: Manage systems Action?
What would the need be for turning characters on and off be, exactly? Are you talking about NPCs or the Player? Again, the more detail and context you can provide, the more help can be given.
I'm using Unity 5.4.3 and the latest package for Adventure Creator.
The older game I made in Dec, so that was probably like 5.1~ Unity
Here's the settings I used like a year ago to get the character to move to a point then teleport:
I was more or less just listing the hacking things I tried to try to get the character to stop doing this.
This is same for NPC characters as well, but obviously my primary concern is the player character.
I'm saying... that if I had to I could just have like a duplicate of every character in every region and turn them on and off but that sounds awful...
So are you saying that this is happening because all Navmeshes under _Navmesh are active?
When you say the character "falls back" onto the old NavMesh, what do you mean exactly? Do they teleport back, or try moving back?
In a test-copy of the scene, try my previous suggestion of removing the other NavMeshes and simply using child Polygon Colliders on the default NavMesh. You can do this by removing the NavigationMesh component from both NavMeshDoor and NavMeshPainting (so that only the PolygonCollider2Ds remain), making them immediate childs of NavMesh, and making NavMesh the default.
I mean falls bask as in walks toward the last spot they were told to move to on the Navmesh prior to the switch.
So I tried that, at least I think I did. I made the polygoncolliders a child of the defaultmesh Making the Navmeshs a child and removing the script.
It did not work at all. Do you have a tutorial up for the new movement system?
"MissingComponentException: There is no 'PolygonCollider2D' attached to the "_NavMeshSegments" game object, but a script is trying to access it.
You probably need to add a PolygonCollider2D to the game object "_NavMeshSegments". Or your script needs to check if the component is attached before using it."
PM me your scene file, Managers, and player prefab as a .unitypackage file and I will take a look at it - I don't think these screenshots are enough to help.
I'm honestly super confused by it.