diff --git a/pkg/app/daemon/daemon.go b/pkg/app/daemon/daemon.go
index 70490aef0..2f1cded7c 100644
--- a/pkg/app/daemon/daemon.go
+++ b/pkg/app/daemon/daemon.go
@@ -39,6 +39,7 @@ const (
 	DaemonKindInsertBreak
 	DaemonKindChangeTodoActions
 	DaemonKindMoveFixupCommitDown
+	DaemonKindWriteRebaseTodo
 )
 
 const (
@@ -59,6 +60,7 @@ func getInstruction() Instruction {
 		DaemonKindMoveTodosUp:         deserializeInstruction[*MoveTodosUpInstruction],
 		DaemonKindMoveTodosDown:       deserializeInstruction[*MoveTodosDownInstruction],
 		DaemonKindInsertBreak:         deserializeInstruction[*InsertBreakInstruction],
+		DaemonKindWriteRebaseTodo:     deserializeInstruction[*WriteRebaseTodoInstruction],
 	}
 
 	return mapping[getDaemonKind()](jsonData)
@@ -330,3 +332,27 @@ func (self *InsertBreakInstruction) run(common *common.Common) error {
 		return utils.PrependStrToTodoFile(path, []byte("break\n"))
 	})
 }
+
+type WriteRebaseTodoInstruction struct {
+	TodosFileContent []byte
+}
+
+func NewWriteRebaseTodoInstruction(todosFileContent []byte) Instruction {
+	return &WriteRebaseTodoInstruction{
+		TodosFileContent: todosFileContent,
+	}
+}
+
+func (self *WriteRebaseTodoInstruction) Kind() DaemonKind {
+	return DaemonKindWriteRebaseTodo
+}
+
+func (self *WriteRebaseTodoInstruction) SerializedInstructions() string {
+	return serializeInstruction(self)
+}
+
+func (self *WriteRebaseTodoInstruction) run(common *common.Common) error {
+	return handleInteractiveRebase(common, func(path string) error {
+		return os.WriteFile(path, self.TodosFileContent, 0o644)
+	})
+}
diff --git a/pkg/commands/git_commands/rebase.go b/pkg/commands/git_commands/rebase.go
index 874cbd809..2d1de707f 100644
--- a/pkg/commands/git_commands/rebase.go
+++ b/pkg/commands/git_commands/rebase.go
@@ -250,6 +250,36 @@ func (self *RebaseCommands) PrepareInteractiveRebaseCommand(opts PrepareInteract
 	return cmdObj
 }
 
+// GitRebaseEditTodo runs "git rebase --edit-todo", saving the given todosFileContent to the file
+func (self *RebaseCommands) GitRebaseEditTodo(todosFileContent []byte) error {
+	ex := oscommands.GetLazygitPath()
+
+	cmdArgs := NewGitCmd("rebase").
+		Arg("--edit-todo").
+		ToArgv()
+
+	debug := "FALSE"
+	if self.Debug {
+		debug = "TRUE"
+	}
+
+	self.Log.WithField("command", cmdArgs).Debug("RunCommand")
+
+	cmdObj := self.cmd.New(cmdArgs)
+
+	cmdObj.AddEnvVars(daemon.ToEnvVars(daemon.NewWriteRebaseTodoInstruction(todosFileContent))...)
+
+	cmdObj.AddEnvVars(
+		"DEBUG="+debug,
+		"LANG=en_US.UTF-8",   // Force using EN as language
+		"LC_ALL=en_US.UTF-8", // Force using EN as language
+		"GIT_EDITOR="+ex,
+		"GIT_SEQUENCE_EDITOR="+ex,
+	)
+
+	return cmdObj.Run()
+}
+
 // AmendTo amends the given commit with whatever files are staged
 func (self *RebaseCommands) AmendTo(commits []*models.Commit, commitIndex int) error {
 	commit := commits[commitIndex]
@@ -302,11 +332,16 @@ func (self *RebaseCommands) DeleteUpdateRefTodos(commits []*models.Commit) error
 		return todoFromCommit(commit)
 	})
 
-	return utils.DeleteTodos(
+	todosFileContent, err := utils.DeleteTodos(
 		filepath.Join(self.repoPaths.WorktreeGitDirPath(), "rebase-merge/git-rebase-todo"),
 		todosToDelete,
 		self.config.GetCoreCommentChar(),
 	)
+	if err != nil {
+		return err
+	}
+
+	return self.GitRebaseEditTodo(todosFileContent)
 }
 
 func (self *RebaseCommands) MoveTodosDown(commits []*models.Commit) error {
diff --git a/pkg/integration/tests/interactive_rebase/delete_update_ref_todo.go b/pkg/integration/tests/interactive_rebase/delete_update_ref_todo.go
index 1969be58e..9bb216cfe 100644
--- a/pkg/integration/tests/interactive_rebase/delete_update_ref_todo.go
+++ b/pkg/integration/tests/interactive_rebase/delete_update_ref_todo.go
@@ -66,9 +66,7 @@ var DeleteUpdateRefTodo = NewIntegrationTest(NewIntegrationTestArgs{
 		t.Views().Branches().
 			Lines(
 				Contains("branch2"),
-				/* branch1 was deleted, which is wrong:
 				Contains("branch1"),
-				*/
 			)
 	},
 })
diff --git a/pkg/utils/rebase_todo.go b/pkg/utils/rebase_todo.go
index 3403eef97..f2b60a097 100644
--- a/pkg/utils/rebase_todo.go
+++ b/pkg/utils/rebase_todo.go
@@ -1,6 +1,7 @@
 package utils
 
 import (
+	"bytes"
 	"fmt"
 	"os"
 	"strings"
@@ -96,6 +97,12 @@ func WriteRebaseTodoFile(fileName string, todos []todo.Todo, commentChar byte) e
 	return err
 }
 
+func todosToString(todos []todo.Todo, commentChar byte) ([]byte, error) {
+	buffer := bytes.Buffer{}
+	err := todo.Write(&buffer, todos, commentChar)
+	return buffer.Bytes(), err
+}
+
 func PrependStrToTodoFile(filePath string, linesToPrepend []byte) error {
 	existingContent, err := os.ReadFile(filePath)
 	if err != nil {
@@ -106,16 +113,21 @@ func PrependStrToTodoFile(filePath string, linesToPrepend []byte) error {
 	return os.WriteFile(filePath, linesToPrepend, 0o644)
 }
 
-func DeleteTodos(fileName string, todosToDelete []Todo, commentChar byte) error {
+// Unlike the other functions in this file, which write the changed todos file
+// back to disk, this one returns the new content as a byte slice. This is
+// because when deleting update-ref todos, we must perform a "git rebase
+// --edit-todo" command to pass the changed todos to git so that it can do some
+// housekeeping around the deleted todos. This can only be done by our caller.
+func DeleteTodos(fileName string, todosToDelete []Todo, commentChar byte) ([]byte, error) {
 	todos, err := ReadRebaseTodoFile(fileName, commentChar)
 	if err != nil {
-		return err
+		return nil, err
 	}
 	rearrangedTodos, err := deleteTodos(todos, todosToDelete)
 	if err != nil {
-		return err
+		return nil, err
 	}
-	return WriteRebaseTodoFile(fileName, rearrangedTodos, commentChar)
+	return todosToString(rearrangedTodos, commentChar)
 }
 
 func deleteTodos(todos []todo.Todo, todosToDelete []Todo) ([]todo.Todo, error) {