Yes, better safe than sorry. If you can't find the missing or broken piece, always assume some of it went into your bottom end. I had a similar problem on my CR125, but instead it sucked the piston circlip out and some of it went down in the lower end. I unbolted the complete motor from out of the chassis, and with the top end removed, I poured parts cleaner into the engine cases and flushed out the lower end like that. Then tipping it upside down and waiting for the piece to fall out. It eventually did, but just make sure your crank rotates smoothly. If it doesn't roll smoothly, chances are a small piece could have gotten into the crank bearing.
Keep in mind this flushing trick is just a cheap trick. Someone else may recommend that you split the cases entirely and search and clean the lower end that way. But, I did like I said above, and have had no problems. Good luck.