After building a stir plate, my first stir bar ended up in the bucket. No problem, I thought, I knew it was clean and had been sanitized. So bottling day came and went well, as did clean up. And then after dinner I flipped on the garbage disposal and was met by quite a racket... stir bar #1, all beat to hell.
When I built my stir plate, I bought a package of 6 rare earth magnets, and now the little pill bottle with the remaining 5 lives in my brew-day box so it's easy to remember to use one to capture stir bar #2 before pitching.
Oh, and the beer was just fine. As long as you cleaned and sanitized, you'll be fine.