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Nope. calibre metadata is either stored by calibre using wired transfers or generated by KOReader on calibre command using wireless transfers.
Documents fetched from any other source will be there but won't get any paired metadata so they will be invisible when doing wireless transfers.
IIRC calibre should be able to rebuild the metadata of the missing files if you use "connect to folder" with the path where your documents with missing metadata are placed.
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