我不能重现这个问题。
我运行cobra-cli init创建了一个简单的Cobra应用程序，并添加了一个子命令foo，得到了以下布局：

.
├── cmd
│   ├── foo.go
│   └── root.go
├── go.mod
├── go.sum
└── main.go

main.go为最小值：

package main

import "clitest/cmd"

func main() {
  cmd.Execute()
}

在cmd/root.go中，我添加了一个PersistentFlag、--threads（或-t）：

package cmd

import (
  "fmt"
  "os"

  "github.com/spf13/cobra"
)

var threads int

var rootCmd = &cobra.Command{
  Use:   "clitest",
  Short: "A simple cli test",
  RunE:  runRoot,
}

func runRoot(cmd *cobra.Command, args []string) error {
  fmt.Printf("This is the root command, threads=%d\n", threads)
  return nil
}

func Execute() {
  err := rootCmd.Execute()
  if err != nil {
    os.Exit(1)
  }
}

func init() {
  rootCmd.PersistentFlags().IntVarP(&threads, "threads", "t", 1, "Number of threads")
}

在cmd/foo.go中，我定义了一个子命令：

package cmd

import (
  "fmt"

  "github.com/spf13/cobra"
)

var count int

var fooCmd = &cobra.Command{
  Use:   "foo",
  Short: "The foo command",
  RunE:  runFoo,
}

func runFoo(cmd *cobra.Command, args []string) (err error) {
  fmt.Printf("This is the foo command; count=%d\n", count)
  return nil
}

func init() {
  fooCmd.Flags().IntVarP(&count, "count", "c", 0, "Count of foo")
  rootCmd.AddCommand(fooCmd)
}

有了上面的代码，我可以运行：

$ ./clitest
This is the root command, threads=1
$ ./clitest -t 12
This is the root command, threads=12
$ ./clitest foo
This is the foo command; count=0, threads=1
$ ./clitest foo -t 12 -c 2
This is the foo command; count=2, threads=12

我可以像这样为root命令编写一个测试：

package cmd

import (
    "testing"
)

func TestRootCmdWithArgs(t *testing.T) {
    rootCmd.SetArgs([]string{"-t", "12"})
    if err := rootCmd.Execute(); err != nil {
        t.Errorf("failed to execute rootCmd")
    }

    if threads != 12 {
        t.Errorf("expected 12, got %d", threads)
    }
}

func TestRootCmdInvalidArgs(t *testing.T) {
    rootCmd.SetArgs([]string{"--arg-that-does-not-exist"})
    if err := rootCmd.Execute(); err == nil {
        t.Errorf("command succeeded when it should have failed")
    }
}

func TestFooCmdWithArgs(t *testing.T) {
    rootCmd.SetArgs([]string{"foo", "-c", "2"})
    if err := rootCmd.Execute(); err != nil {
        t.Errorf("failed to execute rootCmd")
    }

    if count != 2 {
        t.Errorf("execpted 2, got %d", count)
    }
}

这些测试按预期成功：

$ go test ./...
?       clitest [no test files]
ok      clitest/cmd (cached)

您可以在this repository中找到此答案中引用的所有文件。

我想我找到问题了，多亏了Iarsks提供的例子。
我以前的根

func Execute() {
    RootCmd.CompletionOptions.HiddenDefaultCmd = true
    RootCmd.PersistentFlags().IntVarP(&threads, "threads", "t", 1, "Number of concurrent workers, using Stdin overrides this flag")
    RootCmd.PersistentFlags().StringVarP(&delimiter, "delimiter", "d", ",", "Choose delimiter")
    if err := RootCmd.Execute(); err != nil {
        fmt.Fprintf(os.Stderr, "csvutil encountered an error while executing")
        os.Exit(1)
    }
}

我将此函数分解为：

func init() {
    RootCmd.CompletionOptions.HiddenDefaultCmd = true
    RootCmd.PersistentFlags().IntVarP(&threads, "threads", "t", 1, "Number of concurrent workers, using Stdin overrides this flag")
    RootCmd.PersistentFlags().StringVarP(&delimiter, "delimiter", "d", ",", "Choose delimiter")
}

func Execute() {
    if err := RootCmd.Execute(); err != nil {
        fmt.Fprintf(os.Stderr, "csvutil encountered an error while executing")
        os.Exit(1)
    }
}

而现在它工作得很好。