What version of Topo do you have? Check to see if you can download an update. I'm running 4.2.7, haven't bothered yet to update to 4.5.0.

I right click on a drawn route and get a "split in 2" option. Do that twice (for some reason you can't do it everywhere but try different points along the line), delete the orphaned line fragment, then draw in what you want.

If that doesn't work for you, please be more specific. I.e., what exactly do you mean when you say it only allow you to erase from the end of the route and not in between? I suspect that if you try a few different points you'll find places you can do two splits to create a fragment that you can delete.