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Do you need the calibre file/folder structure itself on the shared host? Or would exporting via "Save to Disk" work as well? I expect it's not so much the author folders themselves that's the issue, rather it's the individual folders for each book.
For my save to disk, I use:
{tags}/{authors}/{series} {series_index} {title}
I use tags for genre (one per book). With a library of ~4,000 books, save to disk with the above template gives me ~900 folders versus ~5,000 folders in the native calibre structure.
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