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Ok, just checking...and may I also assume your paperwhite is jailbroken, and that the Collection Manager is installed and working?
I am not at my computer, but I can tell you from memory what I do.
If I have made any changes on the device that I want to make sure are saved, first I start CM on the device, and select Import Collections TO Calibre.
When that is done, I attach the device to the PC with Calibre running. If I am adding anything or have updated anything in my custom column, I then select Create Collections from the calibre kindle collection menu. When that is done, I eject, wait for the Kindle to catch up, start up Collection Manager on the device, then select Import Collections FROM Calibre. When that is done, I exit out of CM, and my collections are correct.
Are you following all of those steps?
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