The brown discoloration is from moisture that was retained under the old shed that didn't come off. Fungus, and/or bacteria can and does leave a brownish coloration to the scales and skin.
If it isn't too pronounced, it should heal up fine if the substrate in the cage is not allowed to get moist(spilled water bowl, etc..) you can dab some anti-fungal ointment under the scale, or even force some underneath by inserting the tube tip under the belly scale and push some in like you would
"toothpaste". Before you do this, you could even "dip" the area in a small container of Peroxide to fight any bacteria, Peroxide also gets under the ventral(belly) scales easily since it is a liquid, and not a thick cream, or ointment.
Also, do NOT let the snake sit and soak in the water bowl, as this will surely worsen the problem. Take the bowl out, and put it in every day or two just for a little while so the animal can drink, then remove it again until the problem clears up. If you do these things, you will surely see some good results in every successive shed.
Since this problem started in the first place from not completely shedding it's skin, the humidity could very well be a contributing factor that first caused this. So next time the snake's eyes get cloudy(opaque) and is going into a shed cycle, put some damp rags, or spagnum moss in the corner of the cage, and cover 2/3s of the cage with something to raise the humidity level. Most colubrids do fine at a humidity level of 50-60%.
Don't moisten things too prematurely, snakes typically shed the skin 2-5 days AFTER the eyes TOTALLY clear up from being opaque, depending on their individual activity level.
hope this helps, ~Doug

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"Better to be silent and thought a fool, than to open mouth and remove any doubt!"