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Some questions:
1) What setting are you using for metadata management (preferences -> add/save -> send to device)?
2) What have you put in the Sony device customization for creating collections?
3) Are the collections you are looking at built from the series column? In particular, are there any tags with the same names?
4) Assuming you are building collections from series, what happens to the list if you send one book from the series to the 505? Does the order change?
5) What version of calibre was used to originally add the books to the Sony?
If you have not manually added collections (all your collections are built from tags and from series), then you can try changing metadata management to automatic then plugging in your sony (plug in the device after you make the change). With that setting, calibre will resend the series and tag metadata to the device, deleting all existing collections and then re-adding collections from current metadata. Please note: when using 'automatic', calibre will delete any collections that were manually added or are not represented in current metadata. Don't change the setting if deleting such collections will cause you unhappiness.
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