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I suspect it is the search which explains no apparent books when there are a bunch of files. It must just not be regenerating the results over the delete and reload cycle.
In all cases where there were books showing in file manager and I needed to delete them, I used file manager to do the delete. When necessary, this was followed by delete all books in CC that don't have files. In all cases, CC was used for the download over a wireless connection to the Calibre on my desktop.
I seem to have a working and maintainable arrangement now, so this report is mostly just to alert you to some behaviors which you may not know about.
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