How do I import a revised script without it throwing off the current list?

Unfortunately that is not possible just within Shot Lister.

But we have partnered with the Scriptation app. So now you can easily send your scripts and script revisions from Scriptation to Shot Lister and Shot Lister will seamlessly import all scenes and metadata and update any revisions. You can also easily navigate back and forth between the two apps making it super easy to reference specific scenes and notations.

If you aren't a subscriber to Scriptation, then you can add revision letters after importing your script if changes are made,  but any changes will have to be done by hand, You can't re-import the script.