FWIW, I have used printed BRPro Poker chips as spacers for flattening. I've done hundreds of chips, and not a bit of color transfer or damage to either the clay chip or the ceramic chip used as a spacer.
While using blanks will remove all concern of color damage, I personally haven't seen any issues using printed BRPro ceramics.
Using 43mm spacers for flattening 39mm chips is definitely recommended, as just a tiny amount of misalignment using a 39mm spacer can leave a strange edge on the heated, softened 39mm clay chip.