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Originally Posted by Steve8x8
-1- Once made invisible, I cannot find books in the CM root anymore to move them, or make them visible again. Calibre doesn't seem to care, but also not to have a way to toggle visibility.
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Menu -> Display Options -> Show invisible items in Home.
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-2- Selection and copy/move options only work for the 5 books in the top panel. Selecting, then scrolling will clear selections. Bug or feature?
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Neither nor. It's a limitation imposed by the Kindle. Because of the severely limited memory on Kindles, CM can only deal with a few items at the same time. Essentially, you can only interact with what you see on the screen. Anything else would result in an explosion of the program logic complexity and memory requirements.
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-3- Making a book invisible will keep me at the same position. Moving to collection will send me back to page 1. Although this resembles Amazon's library: Bug or feature?
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Same reason as above. You only interact with what you see. If you change the collection, you start from "scratch" (page 1).
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-4- I understand that I will have to reinstall Kindlet JB and DevCerts when upgrading (while that should leave the device JB intact) - what will happen to my CM collections in the meantime?
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Nothing
- they're kept.
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-2- and -3- together made it a bit tedious to move *most* books into collections - now that I think about it I should have created a collection "Uncollected", drop everything in my way there, and empty that one when done...
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Menu -> Display options -> Upper pane: show unfiled items only. Well, now you know
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I've still got a couple of days to play with the device, every hint is appreciated.
And... did I say "Thank you" yet? 
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Hope the above helps a bit. And thanks for the kind words