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I just tested FolderOut with an official epub3 epub that uses remote resources listed in the manifest without an actual file inside the epub and FolderOut handled that just fine.
So I am unsure how inside the copy to folder routine that an id can be generated that does not actually point to an existing local file.
What platform are you using?
Are you on a recent Windows version that routinely erases temporary files out from under Sigil? If so you should set your own temporary folder location in Sigil Preferences.
Are you on a recent Mac version that will routinely erase temporary files out from under Sigil if they are left for more than 3 days (ie. Sigil has been running for more than 3 days).
If so, we again recommend you set your own temporary folder location in Sigil Preferences?
Could this ebook have been generated on a Windows machine which does not have a case-sensitive filesystem and then you are running FolderOut on on a case-sensitive system such as Linux or some Mac versions. If so, you could have the file name case incorrect in the manifest item entries?
Otherwise I am out of ideas. It would certainly help to include a file listing of the names of the files inside the epub and a screenshot of your opf. Or alternatively, try running the pubcheck plugin before running the FolderOut plugin as it may detect what is strange if anything about your epub.
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