If you can't remove the whole panel to reposition it, I think you are correct that you'll have to remove a little bit of the bottom edge to get it back in place. If it were me, I'd think about doing the following:
1. Modify the bottom of the panel for a better fit.
2. Drill some more holes in the panel for screws.
3. Apply some adhesive to the back of the panel along the edge.
4. Place some screws in the panel for it to remain flush.
5. Caulk along all edges and screws.
I'm sure some other posters will have alternative ideas here.