What must the sister do regarding the Zakat al-Fitr she gave to her niece who abandons prayer, and is she required to re-issue it after its prescribed time has passed, and is there sin upon the one who suggested that?

One who does not abandon prayer entirely is not judged to be a disbeliever. Therefore, as long as your niece prays, even if she misses prayers sometimes, she is not a disbeliever, although she is in great peril and characterized by wickedness. Giving zakat (definition) to a wicked person is permissible and valid. Accordingly, your sister's zakat is valid if her niece is poor.