Hello, I worked with a product called Anywhere USB, AnywhereUSB - Digi International for exactly this purpose, licensing dongles. It worked very well. I had 3 dongles plugged in there.
I would check with the application vendor first, but in my experience they didn't know what I was talking about...
You install an application on the server where the dongle needs to connect to, install some drivers, then just map it out to the port where the dongle is connected. It was pretty simple actually and worked very well.