If you are doing changes in Hibernate entities itself, you don’t have to do anything else to ensure the consistency of L2 cache, Hibernate will take care of it.
If you are doing changes via native queries, then explicitly mention which entities are affected, otherwise Hibernate will invalidate the entire second-level cache.
If you are changing data in the database from another process, then Hibernate is not aware of it, and you will have to define a strategy that best suits your requirements app (expiration policies, explicit invalidation called from the outside of the application, etc).