@Tex: any more on bug number 2? Are you still able to consistently reproduce it on your end?
Never mind. Apparently, I can't read. You have to have Book View open when deleting the files and not Code View. I can consistently reproduce it on Windows with your Test epub.
But there has to be something else in play ... because I can delete multiple css files from other epubs with identical circumstances (page open in Book View that has both css files linked whenever deleting). Nope. Wrong about that too.
100% reproduceable on Windows.