What application? What instance? Exactly what did you copy? Exactly where did you copy it? NetBeans will only let you pick one of the subdirectories for "server", it will never show you anything else.
I copied an instance, Jboss/server/iopmee from JBoss on a linux machine, Centos, to a JBoss server on my Windows VM, JBoss/server/iopmee. I believed that since I copied over from one JBoss to the other on Windows, it would show up in NetBeans Add Server Instance popup window.
I believe that you are are correct in that I need to ensure that I have exactly the same version JBoss on both machines.
However, I have scraped trying to get it to work on Windows and will just try to get it to run on the Linux machine.