Yes, and no. Yes, if you cut a "stem", and leave a stub, the end of that stub will turn brown. And over the long term, it will die back to where the cut stub joins the branch. And yes, you won't see it, because it's hidden under the remaining foliage.
Here's the No part. Cutting a stem, is more akin to pruning. When cutting a stem, it's more like cutting a branch on other trees on a juniper, the exterior of young stems looks just like a "needle".
If you go back, and look at the picture that Sorce posted, it looks like some needles were shortened. Not stems.
When I cut back, I try to make my cuts as close to the joint as possible and leave no stem.