Replace only some groups with Regex

A good idea could be to encapsulate everything inside groups, no matter if need to identify them or not. That way you can use them in your replacement string. For example:

var pattern = @"(-)(\d+)(-)";
var replaced = Regex.Replace(text, pattern, "$1AA$3"); 

or using a MatchEvaluator:

var replaced = Regex.Replace(text, pattern, m => m.Groups[1].Value + "AA" + m.Groups[3].Value);

Another way, slightly messy, could be using a lookbehind/lookahead:

(?<=-)(\d+)(?=-)

You can do this using lookahead and lookbehind:

var pattern = @"(?<=-)\d+(?=-)";
var replaced = Regex.Replace(text, pattern, "AA"); 

I also had need for this and I created the following extension method for it:

public static class RegexExtensions
{
    public static string ReplaceGroup(
        this Regex regex, string input, string groupName, string replacement)
    {
        return regex.Replace(
            input,
            m =>
            {
                var group = m.Groups[groupName];
                var sb = new StringBuilder();
                var previousCaptureEnd = 0;
                foreach (var capture in group.Captures.Cast<Capture>())
                {
                    var currentCaptureEnd =
                        capture.Index + capture.Length - m.Index;
                    var currentCaptureLength =
                        capture.Index - m.Index - previousCaptureEnd;
                    sb.Append(
                        m.Value.Substring(
                            previousCaptureEnd, currentCaptureLength));
                    sb.Append(replacement);
                    previousCaptureEnd = currentCaptureEnd;
                }
                sb.Append(m.Value.Substring(previousCaptureEnd));

                return sb.ToString();
            });
    }
}

Usage:

var input = @"[assembly: AssemblyFileVersion(""2.0.3.0"")][assembly: AssemblyFileVersion(""2.0.3.0"")]";
var regex = new Regex(@"AssemblyFileVersion\(""(?<version>(\d+\.?){4})""\)");


var result = regex.ReplaceGroup(input , "version", "1.2.3");

Result:

[assembly: AssemblyFileVersion("1.2.3")][assembly: AssemblyFileVersion("1.2.3")]

If you don't want to change your pattern you can use the Group Index and Length properties of a matched group.

var text = "example-123-example";
var pattern = @"-(\d+)-";
var regex = new RegEx(pattern);
var match = regex.Match(text);

var firstPart = text.Substring(0,match.Groups[1].Index);    
var secondPart = text.Substring(match.Groups[1].Index + match.Groups[1].Length);
var fullReplace = firstPart + "AA" + secondPart;

Here is another nice clean option that does not require changing your pattern.

        var text = "example-123-example";
        var pattern = @"-(\d+)-";

        var replaced = Regex.Replace(text, pattern, (_match) =>
        {
            Group group = _match.Groups[1];
            string replace = "AA";
            return String.Format("{0}{1}{2}", _match.Value.Substring(0, group.Index - _match.Index), replace, _match.Value.Substring(group.Index - _match.Index + group.Length));
        });

Here is a version similar to Daniel's but replacing multiple matches:

public static string ReplaceGroup(string input, string pattern, RegexOptions options, string groupName, string replacement)
{
    Match match;
    while ((match = Regex.Match(input, pattern, options)).Success)
    {
        var group = match.Groups[groupName];

        var sb = new StringBuilder();

        // Anything before the match
        if (match.Index > 0)
            sb.Append(input.Substring(0, match.Index));

        // The match itself
        var startIndex = group.Index - match.Index;
        var length = group.Length;
        var original = match.Value;
        var prior = original.Substring(0, startIndex);
        var trailing = original.Substring(startIndex + length);
        sb.Append(prior);
        sb.Append(replacement);
        sb.Append(trailing);

        // Anything after the match
        if (match.Index + match.Length < input.Length)
            sb.Append(input.Substring(match.Index + match.Length));

        input = sb.ToString();
    }

    return input;

Replace code:

var text = "example-123-example";
var pattern = @"-(\d+)-";
var replaced = Regex.ReplaceGroupValue(text, pattern, 1, "AA");

Extension class:

public static class RegexExtensions
{
    [Pure]
    public static string ReplaceGroupValue(this Regex source, string input, string groupName, string destinationValue)
    {
        return ReplaceGroupValue(
            source,
            input,
            m => m.Groups[groupName],
            p => destinationValue);
    }

    [Pure]
    public static string ReplaceGroupValue(this Regex source, string input, int groupIdx, string destinationValue)
    {
        return ReplaceGroupValue(
            source,
            input,
            m => m.Groups[groupIdx],
            p => destinationValue);
    }

    [Pure]
    public static string ReplaceGroupValue(this Regex source, string input, string groupName, Func<string, string> destinationValueSelector)
    {
        return ReplaceGroupValue(
            source,
            input,
            m => m.Groups[groupName],
            destinationValueSelector);
    }

    [Pure]
    public static string ReplaceGroupValue(this Regex source, string input, int groupIdx, Func<string, string> destinationValueSelector)
    {
        return ReplaceGroupValue(
            source,
            input,
            m => m.Groups[groupIdx],
            destinationValueSelector);
    }

    [Pure]
    private static string ReplaceGroupValue(
        Regex source,
        string input,
        Func<Match, Group> groupSelector,
        Func<string, string> destinationValueSelector)
    {
        var matchResult = source.Matches(input);

        if (matchResult.Count <= 0)
        {
            return input;
        }

        var text = input;

        foreach (var group in matchResult.OfType<Match>().Select(groupSelector).OrderByDescending(p => p.Index))
        {
            var begin = group.Index > 0 ? text.Substring(0, group.Index) : string.Empty;
            var end = group.Index + group.Length < text.Length
                ? text.Substring(group.Index + group.Length)
                : string.Empty;
            var destinationValue = destinationValueSelector.Invoke(group.Value);
            text = $"{begin}{destinationValue}{end}";
        }

        return text;
    }
}

go through the below coding to get the separate group replacement.

new_bib = Regex.Replace(new_bib, @"(?s)(\\bibitem\[[^\]]+\]\{" + pat4 + @"\})[\s\n\v]*([\\\{\}a-zA-Z\.\s\,\;\\\#\\\$\\\%\\\&\*\@\\\!\\\^+\-\\\=\\\~\\\:\\\" + dblqt + @"\\\;\\\`\\\']{20,70})", delegate(Match mts)
                    {
                           var fg = mts.Groups[0].Value.ToString(); 
                           var fs = mts.Groups[1].Value.ToString();
                           var fss = mts.Groups[2].Value.ToString();
                               fss = Regex.Replace(fss, @"[\\\{\}\\\#\\\$\\\%\\\&\*\@\\\!\\\^+\-\\\=\\\~\\\:\\\" + dblqt + @"\\\;\\\`\\\']+", "");
                           return "<augroup>" + fss + "</augroup>" + fs;
                    }, RegexOptions.IgnoreCase);