:wave: I have merged a lot of Routes, and when you do so, Trainz, whether it be T:ANE or older has trouble trying to match up anything which is not a perfect Seam elevation wise. It has to do with Mathematics and algorithms with X and Y computer coordinates,
Think of it as a Jig Saw puzzle and some pieces don't play well. :hehe:
Doesn't matter if it is few feet, or several hundred, it will slam one side done or both in a funny way, as you described, so the user has to go back and rematch or contour the change in elevation to make it look more normal.
Also what others and I do if the mismatch is that bad, will add empty spacer Tiles, to allow more transition with the different heights, meaning now you have to texture and add more trackage Scenery etc. This is put off for some folks, they hate the extra work, others get used to it, like me, and pick and choose their battles so to speak.
The link below, has another member discussing Merge issues and possible cause etc......
Hope this helps you a bit.......
https://forums.auran.com/trainz/sho...and-creating-sessions&highlight=Route+Merging