Try to add .clone() to de updateOne function

async(req,res) => {
    await Todo.updateOne(
         {_id : req.params.id},
         {
              $set : {
                    status : "inactive"
              }
         },
         (updateError) => {
              // if updateError exist
              if (updateError) {
                    // print error
                    printError(updateError);

                    // response the error
                    res.status(500).json({
                         error : "There was a Server Side Error!"
                    });
              } else {
                    // if error dose not exist
                    // print message
                    console.log("|===> 🗂️  Data Was Updated successfully! 🗂️ <====|\n");
                    // response success
                    res.json({
                         message : "Todo Was Update successfully!"
                    });
              }
         }).clone();
    }

Latest version of mongoose not duplicate execution

https://mongoosejs.com/docs/migrating_to_6.html#duplicate-query-execution

Since you are using async syntax, put your code in try/catch blok:

async (req, res) => {
  try {
    await Todo.updateOne({ _id: req.params.id }, { $set: { status: "inactive"}});
    res.status(200).json({message: "Todo Was Update successfully!"});
  } catch (error) {
    res.status(500).json({error:'There was a Server Side Error!'})
  }
}

Your async/await should look like this:

async (req,res) => {
  try {
      const result = await Todo.updateOne(
          {_id : req.params.id},
          {
              $set : {
                  status : "inactive"
              }
          },
          );
      }
      console.log('success', result)
      res.json({message: "Todo Was Update successfully!", result })
  } catch (err) {
     console.log('error', err)
     res.status(500).json({error:'There was a Server Side Error!'})
  }
}