I have a issue where I have images on a windows server in a "hold folder", when I finish with my images I move them to a "done folder" on the same volume. If my InDesign 5.5 document(mac) is open those images move to the "done folder", but also leave a ghost file with the same name with 0k. InDesign still see these file as if they are still in the "hold folder". I'm thinking that InDesign has a hold or is accessing the image links when its being copied and locking the image file. How often does InDesign check for modified links?
Links in ID use absolute paths. If the time stamp or file size is different from what is stored in the file for each link it would be condidered modified. If the file is no longer at that location it would be listed as missing. When you open a file ID checks the links (if your prefs are set to do so) and reports modified links and missing links. If a link is missing in the specified location, ID will also search the folder where the .indd file is stored and any subfolders. Having a 0byte file at the old location would be a problem.
The best way to handle this is probably to use File > Package to move copies of everything to the new location. ID updates the links at the same time. You can then delete the original files to avoid duplication.