Quests undone

I've recently just come back and with Nightfall as my only expansion I can only flip back and forth between the original game and Nightfall. I noticed that a lot of my quests seemed to have been removed and/or reset. There are many mission areas that have had their completed status removed even though I have finished all of the Prophecies mission/story. Has this happened to anybody else? Also quests in major cities have been reset too for some reason.

New character?

New quests that were later added?

You think you did them but really didn't?

For mission thing... Hard Mode?

I've had a completed quest in my quest log on one of my characters for over 2 years. Nope.