Review the help document Organization of LabVIEW to know more about the structure of the LabVIEW file system on Windows, Mac OS X, and Linux; as well as for suggested location for saving files when working with the development environment.
If your see that your files are in the correct directory. You should feel free to just remove the warning and continue development. If you are using subVIs that call into files in the Library, try opening each subVI directly from Windows Explorer and managing their individual dependencies. If a subVI has changes to an associated library or file, that will carry over if the subVI is then added to a new LabVIEW Project.
Other options you can try to get your files together are:
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