Blue is usually the colour people pick if sketching in a colour cause photocopy blue disappears when photo copied, and Red is such a dark hue- it translates to black and dark grey in comparison to other colours while most blues appear lighter. See if you can find a photocopy blue to use instead. I think it'd scan nicer
Otherwise if you're worried about pencil not erasing, use a harder lead like a 2H. I use a 2H mechanical pencil for my sketches and I've never had problems when erasing it
Pressing lightly helps too.
Sadly though, scanners aren't all born equal, and to get a decent scanner for art is $$$ and then you need good photo editing programs. I barely get by with my Canoscan 35 LIDE. IT's LED rather that fluorescent which means less colour loss but it still has mass colour limitations