Since you have all your shutil.copytrees and sys.path manipulation at the top level of the test modules, they are executed the moment those modules are imported. unittest likely imports all discovered test modules before actually executing the tests so the set up of both modules is executed in random order before the tests are run. The correct way to perform test setup is using setUp and setUpClass methods of unittest.TestCase. Their counterparts tearDown and tearDownClass are used to clean up after tests. You probably will be able to get this to work somehow using those methods.

However, I'm fairly certain that this entire question is an example of the XY problem and you should be approaching this whole thing differently. Copying the modules and their mock dependencies into a temporary directory and manipulating sys.path seems like an absolute nightmare and it will be a massive PITA even if you get it to a working state. I don't know what problem exactly you're trying to solve but I think you should really read up on unittest.mock and even more importantly on dependency injection.