I wonder if this is the only case where this happened
No - it happened with Iguassu
a. When Argentina made its nomination for 1984 the IUCN recommendation was - "Brazil's Iguazu National Park is clearly an integral part of the area and has been included on the tentative list submitted by Brazil. The Committee should request the Brazilian authorities to nominate their contiguous portion of the area and thereby establish an international World Heritage property
b. The 1984 minutes recording the Argentine inscription state "The Committee was furthermore glad to be informed by the representative of Brazil that the contiguous Iguacu National Park, on the Brazilian side of the river, would be nominated by the end of 1984 so that both parks could constitute next year a transfrontier World Heritage Site
c. In 1985 Brazil nominated its part of the Falls but separately
and it was deferred - the minutes state - "The Committee noted that the Bureau had recommended the inscription of this property and had suggested that it could be considered as a single transfrontier property along with the contiguous Iguazu National Park in Argentina, inscribed on the World Heritage List in 1984. The Secretariat informed the Committee that the Brazilian authorities had requested the Committee to postpone the examination of this nomination. The representative of Brazil explained that the authorities wished to study the points raised by the Bureau in its report. It was further indicated that this nomination could be re-examined by the Bureau at its next session. The Committee accordingly expressed the wish that the property would be inscribed on the World Heritage List at
its 10th session in 1986."
d. in 1986 Brazil again nominated its part of the Falls - BUT again separately
! The IUCN evaluation stated "The Iguassu National Park should be inscribed on the World Heritage List, and should be incorporated as one property with the existing Iguazu National Park of Argentina. The name of the property would become "Iguazu, Iguassu National Park of Argentina and Brazil"
e. This time it got accepted separately! The minutes state "in response to the Secretariat's request for advice on the future listing of this property, the delegation of Brazil indicated its wish to list this property independently, as proposed by Brazil, without any link to the concept of transfrontier site or any other similar concept in force or that might be accepted in the deliberations of the Committee. The Delegation of Brazil also mentioned that Brazilian legislation did not allow for any commitment regarding joint management of national parks. The World Heritage Committee, although it took note of IUCN's position regarding the technical desirability of listing this as one property along with the Iguazu National Park o f Argentina, preferred to list this as a separate property as the Iguaçu National Park of Brazil on the World Heritage List."
So - back in 1986 the WHC preferred to have sites inscribed separately rather than "fighting" further with Brazil with a risk that its sector might not be inscribed at all!! There has I believe been a significant change among States Parties who have come to see that a Transnational inscription actually helps them get their sites inscribed and lets them hang on the coat-tails of another country (also without using up their "annual" nomination since the introduction of limits). The extra work in putting together a combined management plan etc etc is seen to be worth it and the result not as onerous as might have been thought regarding transborder cooperation.
The separate inscription of Paraguay's "Jesuit Missions of La Santísima Trinidad de Paraná and Jesús de Tavarangue" in 1993 is a 3rd example of ICOMOS/WHC suggesting a later combination of separate "similar" nominations. ICOMOS had been successful back in 1983 in getting Brazil and Argentina to pool their originally separate intentions but failed with Paraguay. Herewith the WHC minutes onting the paraguayan inscription -
"The Committee inscribed the site on the World Heritage List under criterion (iv). The Committee invited Brazil, Argentina and Paraguay to consider a joint inscription of the Jesuit missions on their territories. The Delegate of Brazil would welcome a joint conservation effort and
announced that such an initiative was being taken in the context of MERCOSUR
". It never happened of course!
The reality is that once sites have been inscribed, nothing is then going to change. EXCEPT that the UK very "generously" agreed to allow its initial inscription of the famed/iconic Hadrian's Wall to become "submerged" within an ever growing list of uninspiring "Limes" inscriptions!!!