I have used this glue on two planes now (well three, but the FuntanaS hasn't flown yet), a 40-size P-51 and a 28% Laser 200. Both have held without showing any signs of coming loose and I just glued the canopies to the covering, and the P-51 scoots along pretty well. The nice thing about the Formula 560 is that is remains plyable, like silicone. I don't think you need to bother with removing the covering. Just roughen the mating surfaces a little and be sure to clean the joint well be fore gluing.

As far as the covering pulling up, I don't think that will happen, especially if its down nice and tight before you glue the canopy on.