You are self taught and doing a PhD?!
Way to go!
Have you told your supervisor about what is happening to your magnets?
Anyway - you are thinking, I imagine, that if you join two small magnets together you should get one magnet of greater strength - so grinding them down should weaken them?
Conceptually: sketch the field lines for two equal strength bar magnets lined up like so:
... all the lines from the N of 1 go in to the S of 2, and all the lines from the N of 2 go into the S of 1. So what happens to the magnet strength close to the poles of the combined magnet compared with the separated magnets?
You know how permanent magnets work right?