I believe this is happening "below" Embrio in the hardware level somewhere. There is a background thread in the program that looks for the available ports, and updates that list if there are any changes. It looks like for some reason your computer is losing connection with the Arduino and then getting it back.

Before the com port disappears, do you have a good connection with the Arduino with the node values getting updated? Or does the port change after uploading the connection program?

After uploading a connection program, could you open a serial monitor in the Arduino IDE and watch it for a few moments? It should send a steady stream of "upd:..." lines, and an "inf:..." line once per second. Does that stream of information cut out?

I don't believe I've actually tested myself with a Micro. I will purchase one so I can do my own tests, there might be something specific with the Micro that I'm not aware of, I recently had to try using a Leonardo to fix a connection issue with that model, so I won't say for sure it's a closed case. I will let you know if I find something. It sounds like a problem at the hardware level or in the .net framework, but I'm not sure.

In the mean time it's not ideal but you could always work in connection mode on your UNO but then upload the final program to the Micro when the project is done.