Do you mean the warning that is worded like this?
While the project was opening, files were detected within the project package that do not exist in the binder. This may have been caused by a permissions conflict, in which the file system refused the deletion of files from inside the .scriv package that had been deleted from the project binder, or by synchronization between different versions of the project (e.g. on a cloud service).
The recovered files can be found in the “Recovered Files” folder at the bottom of the binder.
If so, when you say they that stuff comes up incomplete or empty, are you referring to the contents of the “Recovered Files” folder? If so that may be nothing to worry about. Given the nature of what causes this kind of problem, this is even to be expected. These orphaned files may in fact be from much earlier revisions, that some cloud system duplicated into your project folder recently from an old device or something.
They are recovered in the off chance that your cloud software messed up and the duplicate copy is actually the better one than what ended up in the binder. But they are safe to delete if they are not useful to you.