@mikaelalind - reformatting the device will erase the identifier file that calibre puts onto it when first plugged in. This plugin matches against that same identifier to identify a device, and each list is associated because of it.
So you will need to remove the "old" device as the plugin knows it, and add the device again (which it sounds like you have done). However did you also for each list make sure it has your "new" device associated with it? My guess is that the lists are pointed to your old device id, not the new one.
If you still can't get it to work, post or PM me your Reading List.json file from your calibre plugins folder. If you still can't get it to work, try creating a new list and seeing if that does. Absolute worst case, just delete/rename the Reading List.json file and recreate your lists again, but you should not need to do that.
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