Can the retractable hardtop get out of alignment?
Yes, it could... but that is not your problem, The top is a work of art! You do have a problem with those panels, whoever been playing with them don't know what their doing, something is wrong with the alignment of the push-pull rods of those panels, (owned mine for 1 1/2 years, use all the time) I would snuggest taking to a GM dealer, (or if you know someone that works on aircraft to look at it) (simple rigging) sometimes it pays to pay! And you'll be happier! Hope this will help sorry to hear! Having a top that don't work is no fun. (just another coupe) Good Luck.