You know an InDesign file is never finished, even if you do save it as 'Final version'!
Get real. You are going to want to go back to InDesign and re-export your ePub (reflowable), because someone noticed a typo or a badly captioned photo.
Can we, save ourselves a lot of bother by grabbing all those changes and slip them into the new version?
Here's how with InDesign CC (2014) — yes you gotta get the latest version.
Frankly, I am only dealing with re-flowable ePubs from InDesign. Not fixed-layout.