Michelle, like in my case, if someone saw some purple amethyst in a necklace but wanted the purple part to be lapis lazuli, I would definitely charge for restringing the necklace and purchasing different beads. Just my thoughts :)
One thing I am really glad I've stated in my custom orders is that the first re-work is free, and any additional re-works are $5. I don't know if that sounds harsh, but I've had more than one custom order where the customer had me re-do (re-string) the piece four times! That's a lot of work! So, while I may or may not implement the $5 depending on the case, that being noted there reminds the customer not to be flippant.
However, I do not make them pay for custom orders up front... maybe I should? I've never been burned, but I guess it could sure happen.