It sounds like they have a set of wrapper VIs around a private assembly. If this is the case, then there's isn't a solution because technically, there isn't a problem. Each VI is like a miniature application. Hence, when a VI is stopped, references normally get closed. There are a few exceptions (like VISA resources), but .NET references aren't one of them. That's why if you have, for example, a .NET PictureBox on the front panel of a VI and you draw something in it, as soon as you stop the VI, the contents of the PictureBox go away. This is by design (and necessity).
The only thing you can do is to keep a VI running all the time so you can keep the reference "alive". This VI's sole purpose is to keep the reference in memory. (Make sure you put a small delay in the while loop so you don't hog the CPU.)
