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Three things:
1) you can control what collections calibre makes on the device, which might be easier than messing with reconversions. Go to preferences -> plugins -> device plugins -> Sony, then empty the 'make collections from' box.
2) metadata management is set in preferences -> send to device. Note, however, that if you set it to automatic, then calibre thinks it is in control. For example, it will *delete* any collections it does not know about.
3) Check the setting of the config option preferences -> save to disk -> update metadata in saved copies. If you have cleared that option, then the metadata changes you make in calibre will not be included when you save to disk (which is what I assume you are doing to "store the files").
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