Lasse,
theoretically it is not a problem to have three modules on your BIM Server, but based on our experience the best is having the maximum of two modules. One for the newest version that is rolled out in your office and one older where you have the projects that haven't been migrated yet.
After all projects have been migrated you can uninstall the older one to have only one module. Having more modules require additional resources.
Marton
Marton Kiss
Chief Product Officer
GRAPHISOFT