Most folks who use a nailer for workholding use polymer nails so as to avoid this difficulty.
MDF is cheap compared to an endmill, my inclination would be to replace it — buy a suitable piece, pull the current wasteboard, clamp together, use transfer punches, countersinks and drills to remake the needed holes.
ahhhh then this isn’t gonna be an economical solution. I hate using them but sometimes when a board is slightly cupped or warped it seems to be the only solution to flattening for milling (besides actually flattening the board.)
I wonder what would be the damage to the endmill if you were to cut 0.1in and hit an 18Ga nail. Many people myself included have hit metal objects like clamps head-on. I can see if there are several dozens that it could be damaging. I have used pin nails in my wasteboard so there are several left in the wasteboard but being so thin, I don’t expect they will cause an issue the next time I decide on surfacing.
Why not just use a sharp nail set to drive the brads further down. If a drill hole next to
a brad is acceptable then surely the hole left by the nail set would be OK as well. Btw, I know, don’t call me Shirley.
I initially mounted my spoilboard with 18g brads when I milled it for the Myers setup. Didn’t get all the brads out when I flip it. Long story short, I resurfaced with a whiteside bit @ .010 per pass and have no damage that I can visibly see in my bit or see in my cut surface.