Some hair follicles go deeper than others. Mainly you want to remove the shiny epidermis. This will allow for brain penetration. It will not affect how well it is brained. It may affect how it looks, though depending on how visible and prominent the hair follicles are. It is a judgment call. Try to go as deep as you can and try to get past them but watch how much you are thinning your hide. If you're thinning your hide more than you wish it is time to stop. There is one point that it is very evident how much the hair follicles are going to show. When it is brained the hide will be milky white. At this point any hair follicles that are going to show on the finished product will look like a 5:00 shadow or pepper all over the hide. Not to fear. Get it on a fleshing beam and work on those areas a little more. Any hair follicles that are left after the hide is smoked, depending on how dark you smoke it, will kind of look like a dirty patch. You're still not lost. You can soak the hide even after it's smoked and take it to the fleshing beam, re-brain it, re-break it and then smoke it again, if needed.
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I think whether you continue scraping or not depends more on the thickness of the hide than anything else. You can scrape through. I usually play this one by ear. One thing I know, though, is that I have less of a tendency to leave hair follicles on the hide if I am able to scrape the hair and epidermis off in one single phase of the process. Where there tends to be situations like this is when the hair has slipped out previous to scraping, but this is no a hard and fast rule either.