To clarify, are you losing the actual images in the project, or just the linkage? That is, does the image appear, but external edits and going back to Hype doesn't ask to update?
Hype copies images into the document, and then preserves a "bookmark" to the original. This is a macOS technology that is conceptually similar to an alias or symlink. Unfortunately the exact mechanics of the bookmark is a black box - I think there are several operations that might make it lost depending on how a file is moved, renamed, or copied.