Such as? We've only had two real revamps to dungeons, really, and there wasn't any retcon as to what happened, adventures won, and things progressed to their next logical state.

VanCleef was most decidedly killed by adventurers, setting up his daughter.

We all saw that Arugal was dead dead dead, he was just logically brought back by those who can bring people back from the dead to go wreak havoc in Northrend, leaving the keep empty and perfect for the jerks to move in.

You could maybe suggest that with the new quests in Scarlet Monastery, previous player victories were retconned, but Im sure Joseph will be addressed when that's changed in Mists, making player victories there not 'retconned' or moot.

I figure the Alliance got control over Stockades, then put Hogger in there, and with the Cataclasym opening up a hole to let elementals through, that was pretty logical progression as well. All of the original bosses in there being gone, I think that's a pretty clear sign that what the adventurers who went in there before did stuck.