For most of our customers the general expectation is that all SWFs in your Flex application (including modules, runtime CSS and sub-applications) are all compiled against the same version of Flex. When you upgrade your 2.0.1 application to 3.0, all SWFs used in the application should be upgraded at the same time.
Technically it is possible, in certain circumstances, to allow a 3.0 application to load modules, runtime CSS and sub-applications that were compiled in 2.0.1. We are interested in getting feedback from developers for whom recompilation of existing 2.0.1 SWFs is impossible or impractical and must try to use these 2.0.1 SWFs in their 3.0 applications. There will likely be many rules and restrictions on how both the 2.0.1 SWFs and 3.0 SWFs should be designed and written.
If you fall into this latter category please contact me ASAP (mchotin AT adobe DOT com) so we can gather your requirements. We are making some last-minute decisions as to how this can work.