A good schematic-to-zip workflow preserves the folder tree. If your schematic is in C:\Projects\Rev2\MainBoard.sch and it references libraries in C:\Projects\Libs\ , the ZIP must maintain a relative path structure; otherwise, when unzipped, the schematic will break (missing footprints).
How a Schematic to ZIP Converter Works: Your Guide to Smarter File Management schematic to zip converter work
Converting to a ZIP archive solves several key problems: A good schematic-to-zip workflow preserves the folder tree