I think I know what you mean by rough scales - sometimes by the time my BP is about to shed his belly scales will feel slightly rough/scraggy from being worn down a bit from slithering around. This is especially noticeable during periods of the year when he's more active and roaming around a lot at night.
It's totally normal and after your BP sheds his scales should be smooth again. It's fine to have rough (but not sharp) surfaces in the enclosure like bark, wood...etc. and it's helpful for your BP to have something rough to rub against when shedding. I'm sure your BP appreciates the extra enrichment from the log and different surface textures as well.
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