I agree this sounds like a whoops; been there and done that. Just yesterday, I made a spike in the sky instead of a subtle landscape change. Yeah the window I agree is a bit small, but it's the same interface since the beginnings of Trainzing time so most of have gotten used to it. Let's face it, typos happen.
In this version the undo function works fine. In TRS2004 and TRS2006, doing an undo or two would lead to weird things happening like splines knotting up, holes and spikes, or other unknown traps occurring which go unnoticed until the route is driven, and by then it's too late to fix. After living with that for years, I've gotten into the habit of not doing a lot of undo steps and work carefully instead.
If you're planning on doing drastic changes, I highly recommend doing a save-as prior to editing. Create a new version, close and open that one to continue editing so that your original is still intact should you decide you don't like the changes. It's called good workflow methodology.