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Two points:
1) Your reply didn't make it clear whether you tried changing the device customization that dwanthy pointed you at.
If you did, and if you are running 0.7.20 or any release before, you won't have joy. Custom columns as collections was added in what is currently called the 'calibre beta' (the sticky at the top of the forum). This version will likely become the production release at the end of this month.
2) If you have set metadata management to automatic, then I would expect calibre to delete any collections you made on the device. Zap ... Gone. It would then add collections based on the device customization.
If you set metadata management to manual, then you might get part of what you want. Your hand-edited collections would not be deleted. if 'by accident' calibre uses the same collection name, then calibre's changes would be merged into the collection. That said, there are significant downsides to this. The first is that metadata changes in calibre's library will not be sent to the device unless you send the book again. The second is that the 'connection' between calibre's collection and your hand-edited one is accidental and may not continue to work.
Bottom line: calibre offers two approaches to collections. Automatic management means that calibre owns the collections and do whatever it wants. Manual means that the device owns the collections and calibre will tread lightly. The other one, on send, is middle ground; calibre take ownership of collections for a book during the moment that the book is sent, then cedes it back to the device.
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