If good judgment isn’t used you could in fact distort the flywheel. But if you tighten the puller, so there is a fair amount of tension pulling on the flywheel, then lift the flywheel, and strike the center bolt of the puller several times, as you would a knocker, the combined force’s may release it. If that doesn’t get it free, using a piece of wood to protect it, give the flywheel a good smack on the side, and repeat the above. If that doesn’t get it off, try a side smack in a different location.
A "Boathouse Repair" is one thats done without having tools or the skills to do it properly.