The main thing to keep in mind about any setting is that it was written by a DM. Amongst DM's, we are all peers. The setting that that DM published is his setting. When you borrow that setting for you own table, it becomes your setting. You are not beholden to any sort of cannon or faithful representation of his setting. You aren't publishing a supplement to his game, you are creating a new game setting based on his setting. So feel free to change things according to your taste. Feel free to let things change and depart from the cannon based on the actions of your PC's. Feel free to subvert the deep mysteries of the campaign and make the 'truths' conveyed about the campaign level secrets in the source books mere rumor so that the characters will continually face real surprises and twists and not merely the fulfillment of established expectations. If the leader of some country is known to secretly be the head Twisted Cult of Pederasty and Talking in Theaters, make it someone else and have it turn out that what the players think they know is merely a nasty rumor spread by his political opponents. If the God of Having the Correct Change for Tolls is known to be secretly imprisoned in the depths of the Black Dragon Dungeon, have it actually turn out to be the God of Little Black Lies in disguise. If the Magical McGuffin is hid in the World's Spine Mountains, hide it in the Fire Swamp instead. And so on, and so forth.
Whatever setting you use, remember that the game belongs to you and your players.
Beware also conflict with the setting ego gamer, who own ands memorizes source books so as to gain an unbeatable advantage on the DM in play and to browbeat the DM with small details supposedly being contridicted whenever things aren't going his way. It's best to remind your players right from the start that they are the heroes, that this game may differ in some details from the source books, and that if they really want to stick to cannon then all the fun and important stuff will be done by emo drow elves and lecherous old men while they go and kill some rats.