I can think of 3 mods that are somewhat close to what you're asking, the 1204 a broken world will probably be the most interesting one for you.
- byzantium alive : a flavor mod that add modifiers to the city and change the flag
- purple Phœnix : an alternate history mod where byzantium is like a second rome but still within the diadochi timeframe
1204, a broken world : this mod focus on the fall of Constantinople in 1204 to the 4th crusade forces and the subsequent fragmentation of the byzantine empire. You can play one of those successor states and reform the empire.
Currently none of these mods are up to date but the last two are still worked on. You can also revert to previous versions.
Addendum : the Ashes of empire mod takes you before the arab conquest and focus on justinian reconquest however it's been a while since i've last played it so I can't way too much about it.