It all depends how you want to prove it, arguments and evidences are on both sides, however if you ask from paper's point of view, than you must stick with the point that Two Nation theory is applicable even after the fall of Dhaka.....

To prove this following arguments would be helpful:
1- The fall of Dhaka was the conspiracy of India (However the truth is it was our negligence that let the Indian conspirators play their role, same is the story with Balochistan today), There are proves that Indian intelligence and government kept funding the separatist elements in East Pakistan.

2- There were Economic Reasons, for instance the foreign exchange earned from Jute of East Pakistan was spent in the development of West Pakistan.

3- Dictatorship, Gen. Ayub further deprived the people of East Pakistan, and Gen. Yahya wanted to suppress the separatist movement by force, and the result is known to everyone.

4- Feudalism of Western Politicians, It is well known that most of the politicians from West Pakistan were feudal lords, (Nawab of Kala Bagh, Nawab Liaqat Ali Khan and so on) and others were capitalists and the richest among all, Sir Agha Khan, I.I. Chundrigar. And the rest were dictators, Gen. Ayub, Gen. Yahya. And West Pakistan was the home to the poor, therefore, their leaders also belonged to middle class. Hence, political strata of Western Pakistan could not digest the leadership of the poor.

5- Obduracy of PPP. In the first ever elections of Pakistan, 1970, Sheikh Mujeeb's Party won majority and asked that the National assembly would be held in Eastern Wing, Dhaka, But, Z.A.Bhutto rejected and insisted that the assembly would be held in West Pakistan. Remember, SHeikh Mujeeb's party (Awami League) won 172 out of 174 seats in East Pakistan and more than 60% votes were won by this party.

6- One Unit farce, When Pakistan was created, the population of East Pakistan was more than that of West Pakistan, but our political leaders were not ready to believe in one person one vote system (Which is the essential in democracy), Hence, strange and funny policies were crafted to keep the power within the ambit of Western part.

7- Linguistic issue. Though, Jinnah, the father of our nation, pointed out that the national language would be Urdu, however, after his demise, the issue of national language was raised by Western Pakistan and they demanded Bangali as a national language. In my point of view, it was far better to announce both languages (Urdu and Bangali) as an official languages than delaying the whole constitution because of this issue. In the constitution of 1956, Urdu was given the status of national language, however in 1962 Constitution both languages were given the status of National language. But it was too late, the sense of deprivation was by than taken roots into the hearts and minds of Bengali brethren. Ironically, what our leaders had done for the development of our national language (a language which is spoken by 6-8% only) is very obvious.

These are some points, by elaborating them you can prove that the theory is still true.

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