How can I remove Organized flag from all my scenes?

There isn’t a built-in automatic option in Stash graphical interface. But in can be easily done programatically using API.

Note
Make a backup of your database first so that you can revert these changes if needed.
Guide: How to make a backup

Run the below code snippet in your GraphQL playground at http://localhost:9999/playground.

mutation {
  execSQL(sql: "UPDATE scenes SET organized = false") {
    rows_affected
  }
}
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