The main piste from Choum to Nouadhibou runs south of the railway lines, so you will have to cross over to the north of the tracks at some point to get to Ben Amera.
Although generally it is not recommend to head north of the railway line due to the potential for landmines, I think the consensus is that the area around Ben Amera is not mined. Nonetheless it would make sense to stay in other vehicle tracks while north of the railway line.
Unless you are really struggling with the piste or are on a very overweight bike, I would much rather ride on the piste than the tracks due to the risk of tyre damage on sharp sections of the track.
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