My partner and I only make alterations before printing, as part of the editing process. But we don't really start on that until each book is finished being posted online. We print it all out, and make sure it flows correctly and looks okay in print, then we make adjustments as needed. It's about the time when I catch things like- the hero's sword disappeared in a panel, so I'll add it in, or something is too small to see in print, so it needs to be redrawn bigger.. or stuff like that.
I don't ever go back and update the online stuff though. I feel like my readers wouldn't notice anyways and would rather see new pages.