Replacing ships after taking control of enemy ports
Available here means ships that are still in your supply. Use only those ships, not ones from the board.

You may find this useful from Page 4:


  Exceeding the Components Provided
  Each House is provided a limited number of units,
  tokens, and cards. If a player is using all his components of
  a particular type, he may not bring additional components
  of that type into play. Units that are destroyed in combat (or
  removed from the board for any other reason) are available to
  be mustered again.