Explain why this bug happens.
How to reproduce it.
Two repair flows: (A) with valid .bak or pre-quest save file backups — recommended, and (B) no usable backups — last-resort.

When you accept and complete the GIC quest “Nitori of Gensokyo” in the Bazaar Betwixt Realms

Nitori will repairs your ship assuming a vanilla ship. but when your ship is a FU BYOS, the repair process will go very wrong.
It make you ship from this


become this

if you haven't complete the “Nitori of Gensokyo” quest, exit Starbound completely and manual copy of your save file:
In your Steam Library, right-click on Starbound.
Select Manage → Browse local files.
(This will open the Starbound installation folder.)
Open the folder named storage, this is where your save data lives.
Inside you will see files like:

1. player → your character save files
   
2. shipworld → your ship data
   
3. bak → automatic backups created by the game

or open the path in
D:\SteamLibrary\steamapps\common\Starbound\storage
(the path will probably look different, especially when you're using openStarbound)

Then, return to the game, finish the quest, return to your ship, and exit the game again.

Well, this is where it gets tricky, but don't worry, there is a way.

1. Exit Starbound completely before touching anything, even in game.
   
2. Go to your "storage" folder again.
   
3. Look for files like ".bak1", ".bak2", etc. These are the backup that Starbound made for you. If you are using OpenStarbound, your backup files are probably inside the "backup" subfolder.

You just need to rename the file and delete the .bak extension, then you can use it like a normal game save file.

Now comes the actual fix.
Inside your Starbound installation directory, there are two important tools:

• dump_versioned_json.exe → converts a ".player" file into editable ".json".
  
• make_versioned_json.exe → converts the ".json" back into a valid ".player".

they are in ...steamappscommonStarboundwin32 or ...OpenStarboundwin if you're using openStarbound, copy your .player save file in these folder.

1. Press Win + R, type "cmd" and hit Enter.
   
2. Use "cd" to change directory into the folder where the tools are located.
   
3. Run the following command (replace with your own filenames):

• dump_versioned_json.exe YourPlayerFile.player YourPlayerFile.json

Now you should see a new .json file appear in the same folder.


Open the new ".json" with Notepad++ or any text editor.
Find this section:
"shipUpgrades" : {
"capabilities" : ["systemTravel", "planetTravel", "teleport"],
"maxFuel" : 10000,
"shipLevel" : 3,
"crewSize" : 2,
"shipSpeed" : 512,
"fuelEfficiency" : 0
},


Change it to:
"shipUpgrades" : {
"capabilities" : ["teleport"],
"maxFuel" : 10000,
"shipLevel" : 0,
"crewSize" : 2,
"shipSpeed" : 512,
"fuelEfficiency" : 0
},


Setting "capabilities" to only ["teleport"] removes the vanilla ship FTL systems.
Setting "shipLevel" : 0 is required for FU BYOS to function correctly.
If you want to temporarily keep FTL travel (without FU’s "FTL drive"), you can leave "systemTravel" and "planetTravel".
Save the file.

Back in CMD, run:

• make_versioned_json.exe YourPlayerFile.json YourPlayerFile.player

This will overwrite your broken .player file with the fixed one.
Copy your backup .shipworld (from before the bug) and your fixed .player file into the storage folder, overwriting the broken one.


Launch Starbound and load your character. There you have it, your ship should now be restored without overlapping with the vanilla one.

ok, the worst thing happened, you do not have any manual backup, and all your ".bak" files are either already corrupted (after the bug) or too old to be useful, then unfortunately there is only one solution left.

1. • Before deleting anything, try to salvage as much as you can from your current ship:
     
   • Break and collect all furniture, crafting stations, containers, and materials.
     
   • Move them onto a planet, into storage chests, or into your inventory.
     
   • Once the ".shipworld" is gone, everything still inside the ship will be lost permanently.
2. Exit Starbound completely.
   
3. Go to your "storage" folder and locate your ship file.
   
4. Delete this file (or move it to a safe backup folder outside "storage").
   
5. Restart Starbound and load your character.

The game will automatically generate a brand new ship for you.
Your old ship layout, decorations, and stored items inside the ship will be gone.
This method is a last resort. You will keep your character, inventory, and planetary progress, but all ship-specific progress is permanently lost.