Yes it will persist a case permanently. Use any of the below shapes where you want to persist a case in a flow
Use Custom activity in "Utility" shape, in this custom activity call "pxPersistCase" activity when "pyTemporaryObject" property value is "true" else exit activity.
Use "Persist Case" smart shape as suggested by CarissaW
As per my knowledge First approach is the best, because before calling pxPersistCase acitivty it will check whether the case is temporary or not by using the value of pyTemporaryObject property. If pyTemporaryObject is true then case is temporary else case is permanent.
Temporary object; only lives on clipboard. Allows a work page to go through flow processing without performing any database operations