How will the fact that Port Elizabeth has undergone a name change affect the commonly utilised name of the town? People commonly adopt their own names or sobriquets for things irrespective of what the official name of the thing is.

Will Gqeberha suffer the same fate?

Main picture: 1810 map of the Baakens Valley before the lagoon was filled in with stone from building sites in Main Street. Note also the paucity of dwellings. Note that the town is specified as Algoa Bay

Historical example
How will the fact that Port Elizabeth has undergone a name change affect the commonly utilised name of the town. Historically Port Elizabeth has already experienced such an occurrence more than once. Firstly within the Afrikaans community Port Elizabeth is commonly known as Die Baai. Will this word be superseded by the word Gqeberha?

I doubt it.

If we dig further back but no less than a century, Port Elizabeth was called the Bay. Why the Bay one may ask? That is simply the name by which Port Elizabeth was always known. Prior to Sir Rufane Donkin naming the town after his deceased wife, all maps stated that this area was Algoa Bay. And that name stuck.

Even when booking a passage by steamer, one did not get a ticket from Port Elizabeth but from Algoa Bay. While the steamer was anchored in the Bay, you had to get to her by paying two shillings and sixpence for the passenger launch fare. People living in the country about to visit town would say, “I am
going to the Bay” and never Port Elizabeth.

Based upon historical precedent, I can conclude that name Port Elizabeth might officially be expunged from the records but in common usage might survive, possibly indefinitely.  

Derivation of Gqeberha
Gqeberha = Kabega (Kwêbêga)?

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Kabega (EC 3325 DC). Khoikhoi name for the Baakens River, which enters the Indian Ocean at Port Elizabeth, at 33 58S, 25 38E. Derived from tkäa, tka, ‘valley’, the name means ‘in the valley’ or ‘valley river’: the Xhosa name for the river, eVeli, has the same meaning.

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eVeli (EC 3325 DC) Xhosa name for the Kabega River at 33 58S, 25 38E. It is derived from English valley and means ‘in the valley”.

According to Annette du Plessis this name originates from the Khoikhoi & San, who intermingled with and had a huge influence on the Xhosa people, as far as language is concerned. They even named the Xhosa people “Xhosa”. Furthermore the clicks in the Xhosa vernacular, stem from the Khoikhoi and San language. Think “Kabega” & “Gqeberha”….. And “Gaibexa” meaning “full of taaibos”.

Source
PE Raper, New Dictionary of South African Place Names (2nd edition), Jonathan Ball, Johannesburg, 1989 Thesis of Jon Inggs, “Liverpool of the Cape: Port Elizabeth Harbour Development 1820-70“, MA thesis, Rhodes University, 1986