I have no idea what’s going on with Resources but I always warehouse my files. I think the way RW is built is if you move things around a bit from hard drive to hard drive, maybe even to another folder, RW can lose track of some resources. Someone else may have another answer and approach.
But … to keep my own sanity I started always uploading my media stuff (images, sound, video) to some other source: Flickr, Vimeo or YouTube, and sound I often just FTP to my hosting company. Player (Will Wodgage, I’m assuming) will work perfectly fine with full URLs to the warehoused location. Short of your hosting company experience a nuclear disaster you “stuff” will never get lost or disappear.
What happens when you try to re-link them. Do they stay or disappear again? Never had this issue except when a folder has been moved or renamed - Resources is no good at keeping track.