Genmitsu lc40 missed steps

"Got a hold down magnet (quite powerful) on Stepper Motor"

The outer casing of the stepper holds the stator windings, so a strong magnet will wreck the magnetic paths within the motor.
In the best case, the magnet will not have also demagnetized the rotor. In the worst case, the rotor will have lost most of its magnetism and will never work quite right again.

"gantry obstructed on home"

Which suggests it does not home properly, in which case the controller does not know where the head is: it will throw soft limit errors, the head will crash into the rails, positions won’t work right, etc.
Fix both of those and see if the situation improves.