This is, unfortunately, a difficult question to answer: our main type site for a pre-Islamic Bactrian city is Ai Khanoum, which was only a city in the Seleukid and Greco-Bactrian eras before being sacked and abandoned (though the citadel was reused later on). Those cities with continuous inhabitation, or re-use, like Termez, Balkh, Samarkhand (which was in Sogdiana but is still relevant to your question) are still modern cities, making excavation difficult. The Hellenistic era cities were also significantly smaller than the modern urban areas, making it really rather hit and miss as to whether a particular excavation will hit something with visible Hellenistic layers. There is also a general paucity of Bactrian urban archaeology, due to the relatively late development of Bactria's academic study, the conditions in Afghanistan, and missed opportunities for earlier excavations.

However, as with most things Bactria related, with the archaeology and written material we do have access to there is some educated guesswork possible. I'll start with my conclusion; I think you'd first speak of cities becoming entirely post-Hellenistic in the Kushan era.

Prior to the establishment of the Kushan dynasty's imperial state, the indications are that Hellenic urban communities continued to dominate those cities that already had established citizen bodies. The huge, huge caveat to this is that we only have a small sample of these communities; we don't know anything close to an exhaustive list of Bactrian cities that had Greek communities across the Hellenistic era. We also know from Ai Khanoum that at least some Greek-dominated cities were razed and not resettled. Our main indication of continued Greek life in these cities is from Chinese sources on the political situation in the 130s-120s BCE and from the relative length that a visible Greek material culture continued to exist in Bactria. We also don't know which, if any, cities in Bactria had continued to be dominated by Iranian-speakers even in the Hellenistic era.

With the emergence of the Kushan state, a new monumental urban architecture becomes visible in a number of sites (Termez, Bamiyan, for example), along with the foundation of new monumental accumulations such as the huge stupa complex at Hadda. This is the birth of a state sponsored Buddhist urban environment in Bactria, which was to become the new dominant model in the region for the next 500-600 years.

This is not to say there is nothing recognisably Greek in the Kushan era. On the contrary, the Bactrian Buddhist architectural style, along with that of nearby regions, has a visible influence from Hellenistic styles. Some Buddhist stupas directly incorporate visible Greek elements with no disguise, such as figures of Atlas or Herakles, or Hellenistic style peristyles. As a result, it's been theorised that Greco-Bactrian artisans were directly involved in the construction of many of these Buddhist monuments, or at least their beautification. This is not absolutely certain, as it's entirely possible that peoples in the region had become educated in Greek styles and practices and could produce it on their own. The contextual evidence to support direct Greek involvement, however, is the known Greco-Buddhist community that had begun to appear in Bactria and the Indus region by the 130s BCE, along with the continued reference to Greek deities in Kushan coinage well into the 2nd century AD.

However, what we are certainly talking about is the end of the Hellenistic Bactrian city. The new Buddhist style, though incorporating elements of Hellenistic art and architecture and Hellenic culture, was very much a distinctive style in its own right, reflecting the interests of the ruling dynasty and also the renewed potency of non-Greek cultural identities in the new era. These are not cities with gymnasia, the stupa and the Buddhist temple are not recognised parts of the Greek urban space, Greek is not the language of power or the lingua franca anymore, Greek is not the language used for epigraphy, there are no propylaia. Even with the incorporation of so many Greek elements into the Kushan city and state model, we are certainly no longer speaking of Greek influence becoming dominant.