Hi @Dee & @Anon, it’s worth remembering that the queen wont lay an egg in a cell unless it’s perfectly clean, the bees wont store honey in a dirty cell either. I think most of the dark color is from leftover pupae cases, including propolis. I notice when I process beeswax, the first thing the wax moth goes for is the dark stuff under the blocks of cooled wax. The dark stuff being a mixture of, I’m guessing particles of pupae cases & propolis.
I would certainly cut my brood comb out after 2 years or even sooner, but not for the reasons stated.