A command line application that takes a folder as an argument, searches for a regex pattern that contains the roman numerals in all the files and converts the roman numerals to numbers.

ConvertRomanToNumerals.cs

using System;
using System.IO;
using System.Text.RegularExpressions;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Threading.Tasks;

namespace ConvertRomanToNumeral
{
    public class RomanNumber
    {
        public string Numeral { get; set; }
        public int Value { get; set; }
        public int Hierarchy { get; set; }
    }

    class Program
    {
        public static List<RomanNumber> RomanNumbers = new List<RomanNumber>
        {
            new RomanNumber {Numeral = "M", Value = 1000, Hierarchy = 4},
            new RomanNumber {Numeral = "D", Value = 500, Hierarchy = 4},
            new RomanNumber {Numeral = "C", Value = 100, Hierarchy = 3},
            new RomanNumber {Numeral = "L", Value = 50, Hierarchy = 3},
            new RomanNumber {Numeral = "X", Value = 10, Hierarchy = 2},
            new RomanNumber {Numeral = "V", Value = 5, Hierarchy = 2},
            new RomanNumber {Numeral = "I", Value = 1, Hierarchy = 1}
        };

        static void Main(string[] args)
        {
            if (args.Length == 0)
                return;
            string path = args[0];

            if (Directory.Exists(path))
            {
                ProcessDirectory(path);
            }
        }

        public static void ProcessDirectory(string targetDirectory)
        {
            string[] fileEntries = Directory.GetFiles(targetDirectory);
            foreach (string fileName in fileEntries)
                ProcessFile(fileName);

            string[] subdirectoryEntries = Directory.GetDirectories(targetDirectory);
            foreach (string subdirectory in subdirectoryEntries)
                ProcessDirectory(subdirectory);
        }

        public static void ProcessFile(string path)
        {
            string text = System.IO.File.ReadAllText(path);
            string pattern = @"(<h.>)(Chapter )([IVCLXDM]+?)(</h.>)";

            string output = Regex.Replace(text, pattern, delegate(Match match)
            {
                return match.Groups[1].Value + match.Groups[2].Value + ConvertRomanNumeralToInt(match.Groups[3].Value) + match.Groups[4].Value;
            });

            if(Regex.IsMatch(text, pattern))
                System.IO.File.WriteAllText(path, output);

            Console.WriteLine("Processed file '{0}'.", path);
        }

        public static string ConvertRomanNumeralToInt(string romanNumeralString)
        {
            if (romanNumeralString == null) return int.MinValue.ToString();

            var total = 0;
            for (var i = 0; i < romanNumeralString.Length; i++)
            {
                var current = romanNumeralString[i].ToString();
                var curRomanNum = RomanNumbers.First(rn => rn.Numeral.ToUpper() == current.ToUpper());

                if (i + 1 == romanNumeralString.Length)
                {
                    total += curRomanNum.Value;
                    break;
                }

                var next = romanNumeralString[i + 1].ToString();
                var nextRomanNum = RomanNumbers.First(rn => rn.Numeral.ToUpper() == next.ToUpper());

                if (curRomanNum.Hierarchy == (nextRomanNum.Hierarchy - 1))
                {
                    total += nextRomanNum.Value - curRomanNum.Value;
                    i++;
                }
                else
                {
                    total += curRomanNum.Value;
                }
            }
            return total.ToString();
        }
    }
}