First of all, Hunne is correct about it being difficult to get the Port set up...IMHO there should be one VP for owners of fs1, that'll let them use the original FS1 VPs, if it's possible, rather than, well, I'm not even sure if I installed it correctly - I followed the instructions but music has never worked properly.
But back to the thread

Try creating a new pilot. Also, if you're using a new enough build, pressing "F3" at the main hall will bring up a black screen with a few buttons in the corner. Try clicking the "show ships" button and see if the FS1 ships are listed there.
Or, go to the campaign room or mission simulator and see if the FS1 campaign or missions are listed. If they are, try 'em out.
The fact that you say "all FS1 ships disappeared" makes it sound like the VPs got installed, but for some reason the "in tech database" tag didn't stick.