My way around this feature is to use the Favorites option and only have those collections showing on my home page that have just the books in them on my device.
I do most of my Collections adjustments on the Cloud where I make sure all books are in at least one collection. It took me a few weeks to get my @4400 books into collections but with the help of Calibre and patience I can finally "live" with the CC but they were a major pain in the ass to get up and running the way I wanted.
And though escwartz suggesed it, not using the collections was not an option. I have way to many books not to use them. Even if I wanted to delete the library borrows from my library, my Amazon purchases alone number around 2500.
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