Generally, perfect glass application isn't a necessity. If you sand into and burn through a glass ripple in the middle of a panel, there's only a couple possible problems.

If the ripple is along a seam, that's not a good one to sand through. Since the wood is obviously discontinuous there, the joint relies on the glass and epoxy.

With a CH, if the ripple is lengthwise in the middle/widest part of the bottom panel, it's possible the panel won't handle the weight of a foot stepping through the cockpit opening. Cross-wise ripples have the underlying wood grain running lengthwise, so it's strong enough to support feet. (I did two layers of glass on the bottom panel inside, since my local river is rocky- I was more worried more about punctures inward, than rupturing outward...)

Another hypothetical worry is that the area that is sanded through is fractionally less abrasion resistant than the area with intact glass. You'll still have full thickness epoxy where the ripple was, so only those special rocks that are deflected by glass but too rough for epoxy will ever be a problem.

And the last maybe problem is that glass that's been sanded into or through reflects light a little differently than perfect glass. If you take pride in the perfect chatoyance of your kayak's bottom, then this blunder will haunt you endlessly.