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@james14 - The auto add folder works like a regular physical 'mail box'. When calibre detects something is in the 'mail box', it goes to the front gate, takes it out and puts it in the current library. If it did not delete it then it would repeat the process ad infinitum.
You may be able to get author and title from the epubs themselves. Check the Read metadata from the file contents rather than the file name setting in the The Add Process Tab and use the Add Books from single directory.
Otherwise you can extract metadata from the file name according to the Configure metadata from file name->Regular expression setting. That may mean renaming files. I add books to a 'preparation' library, in there I correct metadata anomalies, especially making sure Author and Title are correct, etc. Only then do I move the books to the target library.
If you get books from multiple stores, websites etc its probably inevitable that you'll have to do adjustments to get the books into your library as you want them. Some stores are not consistent with their file naming nor the embedded metadata, the latter probably depends on publisher too.
BR
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