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What do the reader apps say?
CC doesn't touch the contents of the book file. However, calibre will to update the metadata, which changes the book. Try saving a book to a folder device on your PC then check if you can still read it with Icecream.
You could also try an epub-to-epub conversion. This often fixes pathological markup in books. You might want to save the original, which calibre will do for you if you don't already have an "original_epub" format.
To be absolutely sure that CC is not involved, you could transfer the book (from the folder device, not from your library) using some other method (file explorer & cable, dropbox, etc), then open the book directly with one of the readers. If this works then I will need the copy that works and the copy that doesn't to find out what is going wrong.
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