Yes, When v4.5 is released we will support the client upgrade from 4.2 and respect the settings.
[update 8th Nov]
Ok, so what about your sequenced applications, will they work? Yes, we expect applications sequenced in 4.2 to work just fine on the new 4.5 client, however, there will always be some edge cases and in those circumstances it might require the application to be unpacked to a 4.5 sequencer, and then saved again (not re-sequenced).
As with previous updates, it is recommended practice to upgrade all the clients first, then the servers. 4.2 clients will not connect to 4.5 servers, 4.5 clients will connect to 4.2 servers.
An application would also need to be re-sequenced (or upgraded) if you wanted to use some of the new features of 4.5, for example, multi-language support, dynamic suite composition, etc.