Perhaps, you can fix it by yourself with
Black Chocobo - FF7 Save Game Editor1. Copy (Backup) your save file to another place.
2. Open the save file with Black Chocobo.
3. Select the "Worldmap Location" of "Location" tab.
4, Put "Party leader" to the central sea from Right Click Menu of the map.
5. Copy "Party leader's X -Y Coordinates" to "Sub's ones" and save the file.
6. Load the slot in Game and ride on Sub.