Railworks America

I am having problems with the trackwork for a route I'm working on. I am using 3D Trains ScaleRail SR_ATSF. The "Mainline" track is that giving the problem.
My route (Rock Island in the Illinois river valley) is double track about 40 miles end to end and about 15 miles has jumped up about 3 feet and about 20 miles has dropped (not all in one big section) down between 4-6 feet this is in both tracks in some places and one track in others. I have spent the time raising and lowering, relaying turnouts and then finding that there's more!! There's always more!
The "Branchline" (which I have used for yards, sidings and spurs) appear to have been unaffected. I like using the SR track but my enthusiasm is (shall we say) dented.
Question: Anyone else had this problem?
Question: If I relay all the "Mainline" in "Branchline" would that resolve the problem?
Question: If not should I relay the Main with another product leaving the "Branchline" in place or should I abandon SR and use something else?
Question: Will I live long enough to finish relaying/regrading trackwork to actually run a Rocket or three!?

All answers be they helpful or amusing will be appreciated.

I presume knowing you that there are backup copies somewhere. Are they all like that?

The Backup had some of these jumps. I had little hair to start with and less now. I am leaving things a day (or so) as the exasperation might just cause me to ....................
There are plenty other things to keep me occupied at lower blood pressure just for now.

John don't freak yet brother. You have multiple track bin errors probably separated by several days. You have backups. Back up the way it is now. You need the track and the track.bin. in case you have to relay. Dude this happens. Ive had it happen and did the relay and restores.
Sort your track by date and write down all the grid numbers. Identify the grids with the bad track and the date they changed. You have to restore the files and the track.bin from the day previous. You will lose track after that point. Before restore take screen shots where the dip starts and ends in editor. After restore go 50 meters before and after the dip and then sever the track and weld it back. This has prevented this from recurring for me.

My root causes from different times this happens were.
1. Using wrong track rule on the main.
2. Laying 4 tracks super elevated at the same time.
3. Relaying cross overs more than 5 times in a session.
4. Snapping curves to straight on the main line.

Many times up to 4am fixing this crap. I feel your pain.

My issues stopped when I started using easements on all my curves and not snapping them.

If your going to relay after you lift. Blow away the switches and redo them. Going forward after a track laying session save and check the main line. This dips appear only after a save not while your working on the track. You might also want to sever the track like 20 meters before and after crossovers. Only on the straights don't sever eased track.

You got this John!

Minerman, thank you. Knowing why this happens is a big relief and half the battle. Knowing how to sort it is the other half.
I have never been an especially patient character although in my working life I was known for sticking it out and finishing when others walked away. This is the approach I have tended to use in this game. It is a wonderful game but there are things and times within it which are exasperating to the Nth degree. You have shown that perseverance pays off.
Respect.