Just two things to add to the idea of glue injection.

Do this after the seal coat. That way any exess glue which oozes out won't give that area a darker coloration.

Use a NEW blade in the utility knife, or a single edge razor blade, or an x-acto knife to make the slit, and slit along the grain lines going right through the middle of the soft spot. fill the bottom pocket with glue and let it set up before flipping the canoe over to fill the top pocket. Gravity helps the glue drip into place this way.

If the edges don't fit perfectly after one side is glued down, you may need to shave a sliver off of one edge r the other (very little) with your utility knife.

The thin slit from a sharp, new blade will just look like a natural occuring pattern in the grain when you are finished.

You'll only need a drop or two of glue if you have a simple delamination. If you have a void or cavity in the middle layer of the plywood you'll need a bit more epoxy to fill it.

Hope this helps
PGJ