I'm a prewasher too and don't use pre-cuts for this very reason!
I have washed Charm Squares through. I just put them in a lingerie bag and threw them in with other laundry or fabric. Just make sure that you separate them first (i.e. don't just put the stack in the lingerie bag).
I know that Moda recommends NOT prewashing their pre-cuts, and I think it's a good idea with long strips like Jelly Rolls that are likely to warp in the wash. However, I've never had any issues washing the charm squares, and I'm sure the same is true with the Layer Cakes (10" squares).
Good luck!
