Actually, from the somewhat unclear description, this could just be the normal world-map updating of the game.
Time passes. Things are not (entirely) static. Once you leave certain areas and advance the plot, certain areas become closed off. If there were side-quests you didn't do, items you didn't pick up: too bad, too late.
In fact, a certain side-quest pertaining to finding ore deposits cannot be completed 100% if you miss a deposit in an area that you visit only once during the game.
I think you can get the best reward even without it, but the fact remains: certain quests can only be completed during specific time windows plot wise. Certain items can only be found from areas that you cannot later return to once you leave.
What was descriped by the OP could be a bug - even with the expansions and fixes NWN 2 is hardly the epitome of coding perfection. But this is a game where the main campaing specifically disallows revisiting some areas and practically remakes others before you can do so again.