Put the 2 plugins in separate directories so they're not co-dependent on a single dll. Or update both plugins simultaneously. We try to maintain backwards & forwards compatibility with the AutomaticUpdater versions, so under most circumstances one plugin can use a newer version of the AutomaticUpdater without a problem.
A 3rd option is to just rename the AutomaticUpdater.dll for each of your plugins. I.e. AU1.dll and AU2.dll.