When you first log into Freelancer it gives you a registration key. If you are like me you ignored it and clicked through it. This key is important because it is your identity. If you have your old profile folder that is only half the battle, you still need this key. When the game tells you about this identification key you can also edit it or enter a old key. This is where you would enter your old key from when we used to play the game. If you do not do this, when you enter a new server, (even if you moved your old profile to it), you will still not see your profile.
I can see peoples keys if the profile is moved to the new sever. So, if you want to use your old FL profile, drop your old profile folder onto the server via Hamachi and let me know. I can then view the profile and let you know what you need to change your key to in your game.
This is untested as of right now, but I only figured it out this morning.