I think Marc was on the money in that you would remove the glass on BOTH sides. You have to do that since the bond between the glass and wood no longer exist. I think your chances of rot are 0 since it was probably made of cedar. You will have discoloration and it will dry out in a day or two in the sun. Consider it a tattoo since your chance of actually matching the rest of the wood is also just about 0. I've had a few of those on my boats where a small fissure goes unnoticed until a dark spot suddenly appears. Unless you sand and varnish every year, these things happen. Nothing more than an annoying chore. But you have to do both sides if its a large as you say and... being a canoe, easy to get at.