Let’s assume I parked my ship in a fleet carrier. While my ship is parked the owner of the carrier terminates his account or crashes the carrier. What happens to my ship?
You can't crash a carrier, it's indestructible. If the service shuts down you get booted to the nearest port. Hopefully, the support guys have their procedure in place if someone nukes their game.
From what I've seen on the support megaships (when a starport is damaged and evacuated) if your ship was on board the said megaship when it gets removed you where send automatically to the nearest station (for free and instantly on login) and a message was inbox saying so.
I guess it should be the same for decommissioning FC.