@JimmXinu - Calibre 6.16 adds a 'recycle bin' in the right-click of delete menu. After updating a fic, the old versions appear under the 'formats' tab.
Don't know if there's any way around this, and personally don't think this behaviour needs to be turned off as most users probably won't be poking around in there. (Plus it may be useful in case of glitches or user errors.) But I thought you should know in case you think otherwise.
EDIT: Also, a quick test (and glance at hidden .caltrash folder in library folder) it seems it doesn't keep multiple copies, so a user won't end up with a half-dozen slightly differing versions.