If this is caused by my suggestion above, do not connect to calibre until you have sorted the collections out. The problem is that calibre will recreate the collections you are trying to delete. That will clash with anything you do on the device to remove them and sync the collections. As you have multiple devices, you may need to do this for all of them before connecting again. Clear the collections that might be causing issues, sync all devices and see what happens.
If you do want to connect to calibre, turn off the collection management options in the driver until you have the collection syncing fixed.
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