I’m afraid I think you might be the victim of a bug in Dorico Elements 2, here. If I open your project in the current version, this is how the instrument change looks in the first clarinet part:
And here it is in clarinet 2:
To fix the staff alignment in the full score layout, I think you can simply create a new full score layout. (Resetting the staff spacing in Engrave mode should fix it, but for some reason doesn’t.)
This version of the project includes a new full score layout where hopefully you will see the staves line up properly:
Bax Phantasy MASTER woodwind etc 4B.dorico (2.1 MB)
Is it an option to consider updating to Dorico Elements 6? If your computer is capable of running it, it would cost around €40/$40 (or equivalent in your local currency) and would bring you a lot of additional functionality.