I’m not sure why you did that. All tracks having the same number is about as useful as having no number at all.
I am pretty much convinced that something went wrong with the converion of this library from the old to the new system.
If you force Plex to use the new system (using the Plex Dance) then everything works as expected.
So we must look at what might have gone wrong with the conversion.
You are not the first to be affected by this.