I confess I don't yet know what to make of that, but it is interesting.
In the Service Manual page 31 shows that there is a 'damper volume adjustment'. Maybe, just maybe, tweaking that might help.
Specifically, that adjustment is on the Pedal VR board.
There's a test procedure that includes that pedal, but it basically just tests whether the pedal switch senses the pedal, and not much else.
Is PEDAL (a setting) ON when the pedal is being used?
The pedal circuit board could be replaced, if we could locate a source for it. That would involve taking the whole 'stand' part off the keyboard part, then disassembling the stand to get at the pedal board. But I suspect that ultimately the pedal board doesn't do more than signal that the pedal(s) is/are depressed, and the fault is not there.
It might be a fault in a major circuit board of some expensiveness, but I'm not even sure of that.
I confess I cannot see what to do. Taking this case to a Yamaha Authorized Service Center might be most wise... but that decision is decidedly up to you.
If I can advise you on any point or option (including the choice of local Y. A. Svc. Centers) let me know.