And for macOS, there is Paul's wonderful drag and drop app (available from Mobileread someplace) that handles things properly. At one point there was something similar for Windows.
Found the macOS epub zip tool app thread with links here:
https://www.mobileread.com/forums/sh...ad.php?t=55681
And something similar for Windows here:
https://www.mobileread.com/forums/sh...ad.php?t=84675