Like I said, start using Sigil as your first step, instead of relying on the hack of converting to create an ORIGINAL_EPUB.
Check your work when editing!
This is now your canonical copy.
You can use one of a dozen different time-machine solutions to version stuff, or just keep a backup of untouched direct-from-source-only-alf-has-touched-this EPUBs. (Many people do this. I do it myself, but with MOBI7/8.
)
That should not be necessary, though -- since you were careful when you edited.
