The focus of The Reshaping of British Railways and The Development Of The Major Railway Trunk Routes was different. The focus of the first was to propose (among other things) that steps be taken in the immediate future to close a large number of lines; the focus of the second was to develop a vision of what the railway should look like in twenty years and what network would be necessary to achieve that vision.
Because of this broad-level look, Beeching's expectation was presumably that it would be followed by more detailed studies, with the possibility that these studies could lead to results that meant that which routes would be developed would change - for example, he brings up North London commuter services, heavily reliant on the main lines unlike those in the southeast, as an example of something that would have to be taken to account in more planning.
Thus the value of Trunk Routes is that it is Beeching presenting his vision of what the railway of the then-future should look like. It is through this vision that we can see why most of the routes "not selected for development" would have closed under his vision, at least to passenger traffic.
Beeching is very clear in his report that he believed the railways had too many trunk routes, and that the number of them that the railway directed trains and funds into could be greatly reduced. This, then, leaves the question of what would happen to those routes not deemed one of the trunk routes of the future.
For starters, Beeching directly states that one of the goals of publishing the report is "so that any future proposals for trunk line closure, or diminutions of line utilisation, can be seen in a broader context". This is an explicit statement of a desire for further closures than those recommended in the Reshaping report (which itself was not fully implemented).
But beyond that, we can see how most of the lines "not selected for development" do not fit into his vision of the railway. First, an important thing to understand about Beeching's selection of trunk routes is that he expected the transfer of through trains onto the selected trunk routes to be total - for instance, he proposed routing traffic from Newcastle, York, etc. to Scotland not over the ECML through Berwick but instead over the Tyne Valley line and then onto the WCML.
Thus, the only remaining traffic on the routes "not selected for development" would be local services. And it is very clear what Beeching thought of local services outside of the major cities' commuter services. He repeats over and over again that the railways need to focus on "bulk movement", and provides maps showing how the proposed trunk route network links all major centres of population. With passenger traffic he is explicit as to the meaning of this:
"The role of the railways will be to concentrate upon the provision of bulk transport over routes of heavy demand, and over medium to long distances... ...while leaving shorter distances and cross country journeys to coaches and the private car."
In other words, railways cannot compete economically with road transport over the non-trunk routes and should not bother.
In addition, Beeching is explicit that one of the key purposes of selecting trunk routes is to reduce infrastructure costs. Singling lines etc. will do very little to balance the books when a line's only left with local services...
