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There is a bug that I just fixed (for 0.7.24) where when using manual management, series collections will often revert from series order to the order they were sent to the device.
If you do not have manually-added collections (added using Sony's SW or calibre's device view), then switching to automatic management will fix the problem. Preferences -> send to device -> metadata management. Note that when using automatic management, calibre is completely in charge of collections. Calibre will delete any collection that it didn't create.
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