The bindings are stored in %APPDATA%\Arrowhead\Helldivers\user_settings.config which is a plain-text file.
You can open it in notepad and remove the mapping for the controller you want to reset.
The default mapping will then be applied the next time you start the game.
If the above did not work you can take these steps to reset controller inputs while retaining progress:
1. Find the Helldivers save folders:
- One is located in AppData, typically:
- One is located in Steam, typically:
C:\Program Files (x86)\Steam\userdata\[userid]\394510\remote
2. Backup these folders
3. In the AppData save folder, delete the files named:
- CAUTION!!! Do not delete the files ending in "_user"
4. In the Steam save folder:
- Open the file named helldivers_save using for example Notepad
- Select everything in the file (ctrl+a)
- Hit delete to empty the file completely
- Save the file (ctrl+s)
- The file should now be 0 bytes large, if not redo these steps
5. Start the game:
- You might get prompted regarding Cloud Sync Conflict, if so select "UPLOAD TO STEAM CLOUD".
- You will need to watch through the intro.
- Press play and you will enter the tutorial. Press start and select "Skip Tutorial".
- Once in the main menu, exit the game.
6. Play the game:
- Controller inputs are now reset and all your progression will still be kept.
7. If this did not work:
- Copy your backed up versions of the saves back to the save folders.
- Start the game and make sure that everything is back to the way it was.
- Restart at step 3.