There has been some great input and I have a couple of ideas. I don't set knots, though have made an awful lot of knives and straight razor scales. A dremel is a great tool if the knot isn't going all the way into the due the a tight fit from the handle. Based on what StubbleDaddy said, that may be much of the issue.
My experience is with marine two part epoxy and you are interested in Silicone, so this may not apply. That said, the marine epoxy is very sensitive to surface preparation. The one I use is one of the strongest bonds in the world, though if you epoxy two smooth surfaces it will ultimately come apart. It requires roughing up the surfaces with extremely course sand paper to give it something to hold onto.
The epoxy is also very sensitive to surface prep, which I do with Acetone and paper towels. The acetone will get rid of any oil, grease, etc... The manufacturer said to use paper towels as the slightest amount of fabric softener will keep it from bonding - that rags around the house may have traces.
I also think there is something to be said for using hot glue on knots. The knot will come out if you use really hot water during use, though it sure is easy to get them out if you want to change knots.
MaineYooper and
keto like this post