ASP.Net C# - Setting a MySQL query and parameters based on a condition

You just have to move the declaration of the cmd outside the if block:

//validation checks
else
{
    string connStr = ConfigurationManager.ConnectionStrings["myConnectionString"].ConnectionString;
    MySqlConnection conn = new MySqlConnection(connStr);

    string questionSource = Session["QuestionSource"].ToString();
    string cmdText = "";

    MySqlCommand cmd; // <-- here
    if (questionSource.Equals("S"))
    {
        cmdText += @"SELECT COUNT(*) FROM questions Q
                    JOIN users U
                    ON Q.author_id=U.user_id
                    WHERE approved='Y'
                    AND role=1
                    AND module_id=@ModuleID";

        cmd = new MySqlCommand(cmdText, conn); // remove MySqlCommand  here
        cmd.Parameters.Add("@ModuleID", MySqlDbType.Int32);
        cmd.Parameters["@ModuleID"].Value = Convert.ToInt32(Session["TestModuleID"]);
    }
    else if (questionSource.Equals("U"))
    {
        cmdText += "SELECT COUNT(*) FROM questions WHERE approved='Y' AND module_id=@ModuleID AND author_id=@AuthorID;";

        cmd = new MySqlCommand(cmdText, conn); // remove MySqlCommand  here
        cmd.Parameters.Add("@ModuleID", MySqlDbType.Int32);
        cmd.Parameters["@ModuleID"].Value = Convert.ToInt32(Session["TestModuleID"]);
        cmd.Parameters.Add("@AuthorID", MySqlDbType.Int32);
        cmd.Parameters["@AuthorID"].Value = Convert.ToInt32(Session["UserID"]);
    }

    int noOfQuestionsAvailable = 0;
    int noOfQuestionsWanted = Convert.ToInt32(ddlNoOfQuestions.SelectedValue);

    try
    {
        conn.Open();

        noOfQuestionsAvailable = Convert.ToInt32(cmd.ExecuteScalar());

        if (noOfQuestionsAvailable < noOfQuestionsWanted)
        {
            lblError.Text = "There are not enough questions available to create a test.";
        }
        else
        {
            Session["TestName"] = txtName.Text;
            Session["NoOfQuestions"] = ddlNoOfQuestions.SelectedValue;
            Session["QuestionSource"] = rblQuestionSource.SelectedValue;
            Session["TestModuleID"] = ddlModules.SelectedValue;
            Response.Redirect("~/create_test_b.aspx");
        }
    }
    catch
    {
        lblError.Text = "Database connection error - failed to get module details.";
    }
    finally
    {
        conn.Close();
    }
}

Just move the declaration of the MySqlCommand outside the if/else blocks so you could use it in the final try where you execute the command

//validation checks
else
{
    string connStr = ConfigurationManager.ConnectionStrings["myConnectionString"].ConnectionString;
    using(MySqlConnection conn = new MySqlConnection(connStr))
    using(MySqlCommand cmd = conn.CreateCommand())
    {
         // Don't need to associate the command to the connection
         // Already done by the CreateCommand above, just need to set
         // the parameters and the command text

         if (questionSource.Equals("S"))
         {
                cmdText = @"....."
                cmd.CommandText = cmdText;
                ....
         }
         else if (questionSource.Equals("U"))
         {
                cmdText = "........."
                cmd.CommandText = cmdText;
                ....
         } 
         try
         {
              conn.Open();
              noOfQuestionsAvailable = Convert.ToInt32(cmd.ExecuteScalar());
               ....
          }
    }
}

Notice also that you should use the using statement to be sure that your connection and your command are propertly closed and disposed.