When the subject is a concealed pronoun, the verb form agrees with that pronoun. In «الشَّمْسُ طَلَعَتْ», «الشمس» is the mubtadaʾ, while the subject of «طَلَعَتْ» is the concealed pronoun «هِيَ». The verb is feminine; the optional-agreement rule for an explicit subject does not apply in the same way.
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Feminine Subject as a Pronoun
Rules of the Fāʿil: Explicit Nouns, Pronouns, Number and Gender
When the subject is a concealed pronoun, the verb form agrees with that pronoun. In «الشَّمْسُ طَلَعَتْ», «الشمس» is the mubtadaʾ, while the subject of «طَلَعَتْ» is the concealed pronoun «هِيَ». The verb is feminine; the optional-agreement rule for an explicit subject does not apply in the same way.