To their credit, Smith & Co., who makes CPES, does not market it as a miracle dope to make sound wood out of rotten wood, although lots of others make that claim. It is a sealer, and does a fair job of that on new wood. It makes a great surface for paints to stick to. But if excess moisture or rot is already in the wood, all CPES will do is better seal it in the wood.
Drilling holes will be no benefit. You will probably be removing good wood and the thinned epoxy will still only penetrate by a tiny fraction of an inch. Kill the rot with TimBor or anti-freeze. Explore with an awl to ensure that no rot lies slightly below the surface. If all seems good, the deeply buried wood is probably fine. Drill a few exploratory holes if you must to satisfy yourself that the remaining wood is good. Then fill the holes so they don’t collect water. There’s no point in making Swiss cheese out of the joist.
After you put in the sister(s), the original joist is basically without a job anyway. If you can sister all the rotten joists, that is the way to go.
Wayne
