When building a guitar or any project for that matter I set aside each piece of scrap wood until the project is done. I also gather up the sanding material dust to use as a filler should the need arise. (As seen below )
One reason this topic came to mind was after I made a mistake with my table saw and cut to deep damaging the first fret position of my guitar neck. I at first panicked that I just wrecked what would have been a really cool guitar neck. Then once I calmed down and got to thinking I realized that I had saved the original piece that I had cut from the head stock and that the grain would be a match to splice into the damaged fret.
Above is a couple pictures of the splice I had to install. It wasn’t an exact match but close enough given the circumstance.
After a bunch of sanding and fret leveling the gouged fret surface looks not to bad and is completely serviceable. If I hadn’t kept the scrap wood from this particular build I would have had to toss the neck and start over.