It would end up in the oil if it was off the chain, but I would be surprised the bike is running ok if the timing chain was damaged.
Please don't take my guess as 100% identification of it being the timing chain though.
I had something similar years ago and studied the parts diagrams for the engine in detail, this helped successfully identified what it was.
A forum community dedicated to Honda XRV Trail Bike owners and enthusiasts. Come join the discussion about performance, modifications, classifieds, troubleshooting, maintenance, and more! Open to all Honda models including Transalp, XR, Varadero, Blackbird, NX400 and more.