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I have a strange problem, whenever I play the Byzantines separate from Turkey and this happened even during age of mercantilism and IIRC also age of reovlutions!
Do you mean that they exist at the start of the game or that they revolt away?
Technically you are encouraged to use IGC in it's own install (copy) of the game, and not play any non-IGC scenarios with that install since it will foobar the setup.
But if the problem is Byzans revolting then check what TAG they are using in the savegame or the text.csv and then remove that entry from the revolt.txt.