OK,
It still seems odd to me that the file is missing, rather than modified, unless the Word file was moved from it's original location, but that's not really the issue at this point. You've just discovered the problem with working with linked text, when you update it removes any changes you make in ID and replaces the current work with the updated linked text. The only good way to work with a linked Word file is to be sure that you have a good set of styles in the Word doc, and their use is strictly enforced, and that all changes get made in Word, not ID.
Since I've never had to deal with this exact situation, what I'm going to suggest may not be the most efficient method, but I think it will work.
Start by making a backup copy of the doc in it's current state. I haven't tested this, and the potential for something to go seriously wrong is pretty large.
Select each story in the document that is linked to an external source and export to InDesign Tagged Text, compact or verbose should make no difference, then delete the story, but leave the frames. Go into your prefs and turn off link to text files, and then finally place the tagged text back into the existing frames. I'm pretty sure this will get rid of the link and your text should be preserved exactly as it is.
Peter