When I’m using alternate mockups I think it works best to create an alternate for all mockups of the original prototype and give them the same alternate name. This way I can easily switch to an alternate version of my entire prototype.
So I would love to have a feature that lets me create and name an alternate for multiple (or all) mockups with a single click.
Note: We use Balsamiq for paper prototyping, so we create A/B versions of the entire scenario and we create a new revision of a specific scenario after we had a couple of test sessions. The old revision we keep because we add our test observations in that revision.