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Sorry, but that is just impossible. There is no direct connection between the series information and the collections. The only connection is if you have both the options set and series as one of the collection columns. And using both of these have no affect on the other.
How are you maintaining the collections? If you do it on the device, you need to not have the collection management options configured in the driver. If you want to use calibre to do the collection management, then don't do it on the device as the next time you connect, calibre will redo the collections according to the options.
Of course, there could be a bug. I'm pretty confident there isn't in this area of the driver. But, run calibre in debug mode, connect the device, let the device jobs run and close calibre. Then post the debug log. And tell me which collections get messed up.
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