How is the metadata missing? Are the columns you use for the Kobo bookshelves still there but empty? Or are the columns completely gone?
The Kobo Utilities plugin has a function to retrieve the collections from the device into a column in the calibre library. It's not perfect as if you used the series or tags columns for collections, it will retrieve these values as well. But, you can use it to populate a column and then edit that column as needed to remove collections that come from other columns.
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