One way to deal with this is by renaming the artifact itself. So for a project foo-1.0.0 with a branch for Initech, instead of trying to figure out how to increment the version, you make foo-initech-1.0.0, and start incrementing its versions independently until you can get back in sync. This seems to work well as long as foo-initech doesn't itself start getting used as a dependency by anyone other than Initech.