OK, I might have a problem after all. I have a crack in the cutaway, running from the corner of the neck pocket. Not sure when it appeared, but it only became obviously visible when sanding back the primer. The curvature of the grain combined with the 90 degree corner seem to have combined to make a weakness. Given that I haven't ever fitted the neck or put stress on this part of the body I assume this has always been present but overlooked. Unfortunately I don't have any good photos of this angle from before today.
Any suggestions? Should I fill this with something? CA (super) glue? Epoxy? Wood filler?
Also, I am worried about this crack affecting the structural integrity of the guitar once the neck is attached. It looks like just the normal stresses applied to this area may cause issues later on.