Thanks everyone, I'm leaning towards leaving well enough alone, ideally having spotted my mistake I'd like to correct it, but due to where I am in the construction, I'm worried I could easily make things worse. Filling the holes will require punching out the captive nuts that were snugged up with epoxy and I can't get at them from the back anymore, to chip it away, so it would be a case of punching them out and hoping the integrity of everything else holds. The 1.5mm discrepancy would mean drilling up 2.5mm of the plug and 1.5 of the ply, the drill will naturally want to follow the easiest path, especially as it will be done free hand, so the holes might not end up where I want them. I could knock up a guide block to try and minimise the risk, but I'm still hampered by working at the end of a tunnel! and won't easily see what's going on.
And I'm reassured by Jon and Mike's considered opinion that it's unlikely to detract from the flight performance.
I think I'll just put this down to experience and something to really think through for the Aurora or Beetle, i.e. the next build
Thanks again.