OrganicMaps (shout out to CoMaps, the OM alternative) and many others use OpenStreetMaps.
This might not be what you want to hear, but you can edit the maps, and the next time OrganicMaps updates, it'll include your changes.
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Are there still train tracks there? There's an option on OpenStreetMaps (which to repeat, is where these apps get their data from) for "Disused Railway". Maybe labeling them correctly would stop them from blending in with other types of trails.
OrganicMaps (and CoMaps) aren't designed around "routes", but instead can be used for navigation without a preplanned route. So that's not really what you're looking for.
You can use one of many services to create your own pre-planned route. I have a Garmin bike computer that I can load a route into and it'll give me basic directions (designed for a small screen). I'm sure something like that must exist for a phone, but I'm not sure. The bike computer also records my GPS track so I can look at it later. I have a program called Endurain running on my server (I'm a nerd) which is like Strava but with fewer features.
Even the Garmin app can create routes, but their maps are outdated in my area so YMMV.