FocusGTD3 supports OmniFocus 3 and it is safe to upgrade the database.
Make sure you have upgraded to FocusGTD3 before doing so.
If you are still using an older version of OmniFocus then please consider using FocusGTD2:
How do I know if I already migrated?
Open OmniFocus for Mac and check the File menu. If the option “Migrate Database” is greyed out, then you have already migrated.