Things to do before Merging a Route(S) Etc

Ok.....If Understood what you said correctly, you have duplication's on the Routes,,,,,
So first course of action:
Route Layer on one, other Route1 Layer named, there has to be Uniqueness across the board........It looks like that is Ok
Next before merging, make sure you have a copy and original.....
Use Copy to play and Merge, always maintain original, I can't stress this enough......

Next
NO consists, of any type on either Route,,,,Never, Never.....I know it is a pain, but I have learned the hard way over years of anguish.....
Next check your Signals, Switches and Area Names, they need to have unique numbers or names....Just take the second Model, and put a 1in front of the names, that'll make it unique to other route.
Make sure you have no missing Assets on either Route, Pure no errors is key here.....
Now make sure, you are in Airplane Mode while you do your merge, I have Carbonite backup and Email, yada yada just like other folks....You want only trainz running, that means if possible, since your in Airplane mode, shut off Virus protection too, if possible, all this stuff going on, can corrupt a file operation, merge etc in Trainz....Been there, done that.....
Now merge your extra Tile,,,,,,,
Now here is what most people fail to due, they don't don't save a copy of this Merge, they continue on working with merged copy....And then save....
Don't do that, you merge, you save, exit Surveyor for a few seconds, then reopen the first merge file, look it over carefully see if anything is wrong????
Now you bring in Module B and merge, wash rinse and repeat the steps......
You should be OK now,
Re add your Rolling Stock etc, connect your Track.....I just throw in a quick Track between the new modules, to see how things run......Doesn't matter if it is hanging in the air etc, quick and dirty is the name of game when checking to see that your basic functions are working between the newly merged Routes.......
Also go into to your
FIND OBJECT option, pan thru industries and Switches Signals etc, see how the names look, see if everything is there.......You rename stuff later, you just want to see if things are basically in order.....And believe me, using Find Object is one of the best friends you'll ever have trying to find things quickly, doing naming conventions and the like....
And of course your
Content Manager......
I wish you good luck here and hope my notes will solve the issue at hand.........
Good Day Sir......