These suggestions are right on. If you absolutely are going to replace that quarter, then you could remove it pre-blasting. But I left mine on during blasting, to help the stiffness of the surrounding structure (basically, to ensure that nothing warped or flexed during blasting). I just told the guy that I was going to replace that quarter panel, so he did not waste labor time blasting it. If your blaster guy knows what he is doing, the job should be thorough, whether the quarter is on there or not.
And I had mine coated in epoxy primer (PPG DP-90), because it sat for over a year before bodywork. The epoxy primers are outstanding, and really seal it up. Most of it will be sanded off during bodywork, but the stuff is excellent to work with. I had a bodyshop clean/vacuum/prep my car, and shoot everything with the DP-90 after blasting...I think it was a couple of hundred dollars, and well worth it.
-Tom