You are correct that you can't epoxy the magnet back together. Once broken they each for separate poles which can't be re--aligned by gluing.
Yes, you can use other magnets and reshape them by sanding or filing. If you do this, replace both magnets so they are matched. The motor won't run well (if at all) with one old and one new magnet. Symmetrical spacing is the most important thing - make sure that the arm has the same gap on both sides when you are done. If it doesn't spin smoothly it probably won't run well...or it will scream and burn up.