Trainz 2019 not saving changes to my session.

Trainz 2019 isn't saving changes to my session. I changed messages I gave trains coming out of a portal, because tracks and trackmarks were deleted to reroute the tracks and I gave them new tracksmarks and orders to follow, related to the reroute, but when I save them, the trains get stuck coming out of the portaals because they still have the same messages they had before I edited the session. Also, I deleted a block of land that had the old tracks on it, but the game still thinks the old tracks and trackmarks exist.
Why won't it save the new messages in the portals? Do I have to replace the portals? I hope that's not the case because these portals had a lot of trains with a lot of messages...

There is some confusing information in this and I may not fully understand what your problems actually are.

It seems to me (and I could very easily be wrong here - not unusual!) that the first place to look is in how you are saving and loading the route and sessions. Portal controls are normally saved as part of a session, not a route. So are you loading the Session each time or are you just loading the Route? (the dumb questions have to be asked first)

You have an older build of TRS19 which did have a fault with this. Delete missing assets did clear the ghost TM's names.