Without hearing the noise it’s very difficult but this may be of some use. I always store my bike upright in a front chock and use a scissor jack under the rear subframe to raise the rear wheel off the floor.
The other day I was cleaning it after a ride and when spinning the rear wheel heard a new clicking/clonking sound coming from somewhere. Very weird. Not a nice sound if you know what I mean. It sounded like maybe the final drive, but maybe in the gearbox too, seemed to travel depending upon which side of the bike I put my ear to. I established the noise was cyclical and very carefully I could just
feel ever so slight a resistance or let’s say something odd somewhere in the drivetrain and the rear wheel seemed to jump the tiniest amount.
Same as you I was fearing the worst. Chipped tooth? Bearing? Anyhow, I couldn’t suss it out. I took the bike out again another day, rode perfectly. Got home. Up on the stand, clicky/clonky noise. Damn it.
Lay on the floor under the bike thinking what could it be? I spun the wheel and with fingertips felt the disc and noticed a very small but rock hard pinhead of something, with my fingernail I could pick at it but it would not come off. (Think of a bit of welding splatter that kinda thing). I had to get a sharp blade and scrape it off, it pinged off. I used a bit of fine wet n dry to smooth some light scratches I made getting it off and the noise has gone.
I did note if you tap the disc with a small metal spanner it really rings, like a bell, I think, maybe, the object was causing the disc to ring aswell as making a click when the pads went over it, which was then transmitting down the transmission amplifying the noise.
As I say, might be nothing whatsoever to do with your issue but it was a new one on me.
