Will a toilet flange bolt cause a problem if dropped into the drain pipe?
It's probably not an issue. There's a very small chance that it will get caught on a fitting and cause a clog, but more likely it'll either settle somewhere forever or make its way to the septic or municipal sewer. If it does clog a simple auger job should clear it.

Years ago I had my drain augered and the guy dropped a full size Vice-Grip down my aging 3" cast-iron pipe system. He tried for half an hour to retrieve it (magnets not being an option) but was unable. I figured it would come back to haunt me for sure, but it never did.