I guess I could have typed that out more clearly. What I was trying to say was: old rod or new rod, do all measurements with the existing bolts and nuts. But assemble ONLY with new bolts that have never been tightened before. Putting new rods in your R6? Purchase 8 additional bolts and nuts.
All I can add to this is, rods are cheap compared to R6 valves, and I saw many "cheap" rebuilds on R6's throw a rod when we ran AMA. So I replaced those cheap rods and never had a problem when we raced, and I'm pretty frugal. A set of rods is literally the same price as a set of tires which won't last nearly as long as those rods will. FWIW, I bought used valves and new rods when rebuilding Tyler's R6 when we raced.
Ah, well there you go, bolts are one and done deal like said. Once they've been stretched they are no longer as strong as they once were.