Hello Simon,
You are right - the latest version of Logic Pro X seems to be unable to correctly import Environment Layers and randomly cables the contained elements, so right now, your only option is indeed to re-cable the entire Environment Layer in your own Logic project.
I have also replied to your support request and attached an example project, which should show how to set up one VE Pro instance with f.i. two multitimbral instances of Kontakt.
Best, Marnix