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I have found that the PRS-505 is prone to losing Collection data if for any reason it crashes (which is not that infrequent) while reading a book. It seems to lose the collection data from the device (memory or card) that was active at the time of the crash.
I would do it the other way around - get the Tags and Series correct in calibre and then delete/resend the books back to the PRS-505. The collections would then be recreated. At least it then become easy to recreate the collections if they are lost again.
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