Hi Stephanie,
One of the possibility may be to start each project with a sort of "master test" that will check the version in the registry and pass or fail according to the version under test.
Additionally you may design a small project that will start your Project Suite and set some variables of the Project Suite according to the version number or whatever may be a condition to run a project (or a part of the project) or not.
I don't know how big are the differences between the version of your software, but this may also help you to design tests with a behavior adapted to each version.
Christophe