I did that on my Chandler Jackson style neck. Part of the problem was not using a drill press and so the drill bit with the hand-held drill kind of went on a misguided path somehow. I then used JB weld glue to fill where where it went through, then was able to redrill and not go through the cavity. Over 20 years later and I have never noticed a problem from it yet, although it's a scar on my perfectionist attitude. Some other guitar projects that I smashed to pieces also remain a scar. Out of sight, but not out of mind, at all.
I had to scrap a made from scratch maple fret-board (sized the board and slotted myself), cause things went a little too slow and problematic when using titebond (did the following ones with epoxy and avoided the problem) But that maple one, was my very first board replacement.
On one of my earliest fret-jobs, I sanded through the fret board into the heel end truss-rod nut hole. Luckily, it was my own guitar.
I guess I thought the more "fall away" the better or something. I'd really like to go back just to observe how that went so wrong, it's still a mystery.
All those really bad ones, that make me want to smack myself in the forehead when thinking about them, are from my late teens/ early 20's.
Worst that happens these days are some minor super-glue run-off accidents and stuck 'half way there' truss rod added washers (but I think I'm at the point where the slightest hint of a problem makes me mod them to be more easily removable)