Originally Posted by mm43
Regarding books are you talking about the whole book folder ( for each book) or just the Epub file?
Also with calibre if I copy all my 500 books in calibre to a master Books folder are they recognised if I add them elsewhere? Or are they calibre files?
You just need to backup the epub file.
I really only use Calibre for converting books, but as I recall Calibre works a bit like Aldiko. When you add a book into Calibre it copies the epub file into it's own folder, but it leaves the original epub in place. The copy Calibre makes is just a copy of the epub. Calibre doesn't do anything weird with the file, it just creates two extra files for each book (cover.jpg and metadata.opf) that contain info about the book. You don't need to back these up as Calibre will just recreate them the next time you add the book. Actually Aldiko also creates these two files when you add a book. have a look in the eBooks folder on your N7 and you'll see those files.
When you read my comments about storing books you need to bear in mind that I'm an old time computer nerd and for me a book is an epub file that I can save into some directory using Explorer. This the complete opposite to the approach taken by e.g. iTunes because iTunes hides the file details from you and you're not supposed to worry about where iTunes has stashed the file. Calibre and Aldiko work a bit like iTunes, and if you're happy for them to work this way that's just fine. use calibre to manage all the books, and use Calibre to copy them to your N7 as required (I'm pretty certain Calibre supports Aldiko on Android). My own preference is to manage the books myself using Explorer and independantly of any software. But this is more work and you do need to be more of a geek.