This
Although I always have a huge honk from my brakes I'd much rather they be silent.. And because of flex I aint putting a disk on my stock
Back to OP though, this does happen, and you might never get sound back. all you can do is pray that when it beds in, fresh grind, and it might sort it out.
It might be that your old rim had an angled sidewall? and the brake pads are no longer hitting square, or the new rim has an angled sidewall.
If that's the case either wait until it beds in or do some sanding