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Just to confirm: which file is the Calibre database itself? Is it the metadata.db file? Is there anything else I need to copy over?
I installed grsync and did the laptop->flash drive->computer sync, and could see that it mostly moved only new books since my last export/restore (along with a bunch of metadata files in the ebook folders, and inexplicably some EPUBs that are very old--dunno if the folder name changed or if rsync detected some file corruption, or what). But Calibre itself is not showing any of the new books. I opened the metadata.db file in a sqlite browser and I can see none of the new books are in the data table, so I'm assuming that file failed to copy over for some reason.
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