The thing is shia and sunni back then are not the same shia and sunni today. First the shia are completely different Ismaili and Twelvers are different. Iran doesn't go around celebrating the fatimids.
This is an interesting note - there's no real Shi'i state anywhere but I imagine the lingering influence of the Fatimids means that the most prominent Shi'i school is still the Hafizi Isma'ilism that was the state religion of the Fatimid Caliphate. Even if the Fatimid Caliphs were never that interested in converting their own populace to their brand of Shi'ism, they still set up madrassas and served as sponsors of Shi'i scholars. I wonder if TTL will also see the death of the Hafizi Isma'ilis with the fall of the Caliphate or if they'll pop up elsewhere like the Nizaris managed to do IOTL.
Maybe a member of the last caliph-imam's family flees to a state on the periphery of the Muslim world, following the pattern established by Abd al-Rahman in Andalusia? Yemen (or maybe even just South Yemen alone) might be a good place for Isma'ili Shi'i thought to hold out against the setbacks: the OTL Isma'ili Sulayhid dynasty in Yemen was enthusiastic about conversions during the time it ruled the area. There were constant battles between the Zaidis and the Isma'ilis there OTL, but with enough hegemony that could be put to relative rest. An ATL Isma'ili warrior-queen putting her own name in the Khutba like our world's Arwa al-Sulayhi would be cool.
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