@senna541: When you buy a new Freighter, the old freighter is replaced, because you can only have 1 Freighter. This will also delete anything you had built on your previous Freighter, including any Fleet Command Rooms you may have had. You basically start with a completely new default layout of your Freighter base.
Your fleet of Frigates should transfer to your new Freighter, so any Frigates you owned before, should still be there. You may however not be able to access the Fleet Missions again, until you have rebuilt one or more Fleet Command Rooms. The below is the message you will get from the Navigator when trying to access Fleet Missions without any Fleet Command Rooms:
I think, or at least hope, that once you have rebuilt one or more Fleet Command Rooms, your issue will be solved, with full access to your fleet of Frigates to send out on missions again. It may even be possible you still had a fleet on an expedition, which you will then be able to debrief as well.