If you don't get the valve timing right you'll do big damage. If the pump timing is out you may get a strange coloured smoke (can't remeber the colour, sorry) but if it's retarded you get no powerm if it's advanced you'll get noisy deiseling and negative work, it won't damage anything in the short term other than your pocket but it's not a good idea to leave it.
However, why would incorrect timing affect one cylinder :-k