Do you have any idea what actions may have lead to this? I agree with you that image files disappearing from within the project is a large problem and I would like to help you retrace steps to find out how exactly this occurred.
Was this a project created in the 3.0 beta, or was it carried over from a 1.9 project that was upgraded? Have they disappeared from the folders in File Explorer as well, or are they just missing when viewed from within Scrivener?
Any more information you can give us on this would be greatly appreciated.