I see each published adventure as a set of guidelines. I throw out/add in encounters, change names and locations, whatever it takes to make the adventure fit the campaign, PCs, and my and the players tastes. The current mod I'm running, The Prince of Redhand, I didn't want to change a lot because it's incredible as is, but the players are doing some unexpected things (I love it when they do that, it doesn't happen often enough in APs) and I find myself reacting on the fly. The last adventure, Spire of Long Shadows, got a complete facelift, though I doubt I need to go into why.