Hype copies all assets within the .hype document file. Any files external to this are only linked so that if they are updated Hype can ask if you want to replace its copy with the newer one.
If your document no longer has images in it, something else might have been going on while writing (especially if you ran out of disk space). If you have a Time Machine backup, that would be the easiest way to get back to a working version.
(If you still do have all assets "emergency restore" procedure would be to control-click on the .hype document and "Show Package Contents" then drag all assets into the Resources folder.)