It should still work even if the magnet is scored up. Bulging is the bigger problem but I don't think Eheims are prone to that.
Muriatic acid will eat the stuff in minutes, but the stuff is nasty to work with. You'd have to get it at a pool supply place, Home Depot and Rona don't carry it. You'd want to dilute it and do it in a well ventilated area - avoid breathing the fumes. Did I mention it's pretty nasty stuff to work with?
