im pretty sure that engine doesnt have to be pulled to change the alternator. i dont know what body or engine you have, but i dont know that ive seen ANY car that requires you to pull the engine to change the alternator belt.
it sounds like youre getting screwed by your mechanic...its time to find a new mechanic.
when the alternator goes bad, your battery wont stay charged. if the belt is getting hard (as aging rubber often does) you will have a squealing noise...not a knock, unless the belt is frayed and is slapping against the underside of the hood.
will it knock when sitting still, at idle? if so does the noise seem like its coming from inside the engine? you should be able to see the alternator just look at the engine. it will look something like this:
what was wrong with the first engine that they removed? do you keep up on oil changes?