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Ok having replicated this about 6 times I think I know what is going on.
Essentially, the news rss download is interrupted so Calibre writes a partial metadata.db-journal file and does not complete writing to metadata.db.
What I end up with is 3 corrupted files: the rss epub, metadata.db, metadata.db-journal.
None of these files will delete, my immediate fix is to rename the calibre folder, create a new folder and move everything but those three files to that new calibre folder. I then place a back-up metadata file so Calibre boots again.
However, I am left with 3 corrupted files that are locked to unix user/nobody. I have found that ftp in to my drive from outside my network allows me to delete them (resolves permissions issues because it requires a log-in).
I guess there is no real fix here, if a rss download is interrupted (loss of connection, my wife opening facebook and the download stopping) then these files end up this way. Its just a frustration because if I dont do as I stated above, the computer just crashes when I open Calibre (and dropbox since my calibre file is synced, and it wont sync corrupted files).
---end of rant---
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