If you are using watersoluble glue, just soak the area until the glue releases. [might take some time] Then re-adjust and squirt in some glue to set: the bead and cove you're using will allow quite a change whereas butt-jted might not have without gaps.

Using a steam iron over a wet cloth might speed up the glue softening - I've 'ironed on' veneer after coating with yellow glue. Getting the heat through a thicker layer might be helped with more steam. Once things loosen up, a stick propped from the inside could push things into shape.

BTW, if it's not a big 'mis-shape' I wouldn't worry about it at all. A 3" length that's a fraction of an inch off won't make the boat handle any differently. When I pulled patterns from a (good) commercial kayak, I was surprised how asymmetric it was!