From what I call my "timeline-to-be" with the current name idea being "the Tsar, the Kaiser and a Springtime Revolution".
The Flags for the three current claimants for the legitimate government of South Sudan:
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The Flag of the Republic of South Sudan (also the Flag of South Sudan OTL), the internationally recognized "legitimate" government. Currently still holds the International Concord seat, and operates as a government-in-exile in Egypt. South Sudan ITTL, gained independence from the (Socialist) Democratic Republic of Sudan in 1977. The government fell to a socialist insurgency 2015-2019, as the fall of the Africanist Republic of the Congo (Saddam/Assad analogue followed by war on terror/civil war) kicked off several widespread insurgencies in Central Africa (2015 was a rather eventful year for TTL actually, there are more stuff), with two being rather active in South Sudan. This government lost last of the ground it controlled in 2019. (The legitimate, capitalist government)
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Flag of the Social Republic of South Sudan which was fully established in 2019. It is recognized by 7 sovereign states (Chinese Social Republic, its 5 puppets and American Socialist Federation) most of which are themselves partially recognized but with International Concord memberships (that said, West Zambia only barely managed to get a membership). Also called "Southeast Sudan" (because East South Sudan doesn't roll off the tongue) This flag is also used by the African Peoples Liberation Army-South Sudanese Section. (*Maoist Chinese Client State)
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Flag of the Democratic Peoples Republic of South Sudan (Southwest Sudan, naturally). The state is barely recognized (only recognized by the insurgent state of Democratic Peoples Republic of the Congo and the Central African Democratic Peoples Republic), lacking the crucial Chinese recognition that CAPDR managed to get due to the lack of an active *Maoist group in the Former CAR. And acts as a puppet state and base for the Peoples Revolutionary Army of the Congo (the people behind DPRotC, likely the closest analogue for ISIS ittl). With European Council sending troops to Chad and Darfur it is believed that the days of PRAotC and its two puppet states are numbered. (The OTL symbol of Zaire is used by the PRAotC and their puppets) (puppets of the extreme Khmer Rogue/North Korea style terrorists)
Other posts in this thread from the same timeline: