Are you by any chance using the Master Documents Feature in Microsoft Word? Read the article at the link.

John McGhie put it succinctly when he said that "there are two kinds of Master Documents: Those that are corrupt and those that will be corrupt soon." It was reported fixed in Word 2007, but "The jury is in: The Master Document feature in Word 2010 remains word processing's answer to Conan the Destroyer. Use it only if you enjoy pain and frustration." Microsoft Word 2010 Bible by Herb Tyson, MVP.

If so, you need to rescue what you can and try a different strategy.