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Backup is not the same issue as (2-way) Sync.
For a GREAT backup, you just don't want any files 'in use' (write locked) or the get skipped, and metadata.db is one of the most important of the set to have.
The thing is, I don't know of a VALID calibre action that leaves those crumbs behind.
Delete wipes everything. No record in the GUI. Nothing
Remove a specific format would leave the cover and OPF (and other formats).
There is an Auto-delete feature for items with the TAG of News, but that triggers AFTER a send
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