This used to happen on the PC version which I also have but not the Xbox version, they fixed it before porting over. (At least it wasn't wiping my route from the galaxy map last time I was exploring which was late Thursday.) The route us still there if you look in the galaxymap, just the next system is not targeted after targeting in the system map. I have been going back in to the galaxy map and having to select the next system in my route. As long as I don't target anything it is fine and I can continue on my plotted route. But what is the point of that if you are exploring? You have to select other planetary bodies to detail surface scan them.
In the PC there is an option to bind a control to re-select the next system to continue on your route without having to go through menus or go back to the galaxy map. I basically want the option to bind this function to the Xbox controller, or have the devs map it for us in the present controls. Makes exploring more streamlined than having to constantly go back and do it manually every time you scan a planet.