Don't just cut them off. I would drill new holes at the top of the bottom slots, fit the new bolts - not tight at this stage, remove the original bolts and raise the motor then seal and tighten all of them. If as you say, it needs to go up two holes, from the looks of things the motor bracket should then be clear of the current bolt holes which can be refitted. If they will interfere in the new position, I'd remove the engine entirely to allow fitment of some countersunk head bolts under the bracket. Make sure you check inside the hull for enough room above the existing bolts to fit the new ones - you don't want to be drilling in at a height where the structure of the well prohibits installation of new fixtures or worse.