How to Regex replace

You have not given any flavor of regex, so I chose my own (C#) in this solution.

A possible approach is to replace tokens in multiple loops. The C# regex allows to globally replace patterns (this covers the and/or tokens). To overcome the limit that regex cannot count, you may apply lambda expressions that count up a variable that is defined outside of that lambda expression.

E.g. a crude version of this could be coded in C# like this:

static string Translate(string input)
{
    string result = input;
    result = Regex.Replace(result, @"\b(and|or)\b",
                           m => m.Groups[1].Value.ToUpper(),
                           RegexOptions.CultureInvariant|RegexOptions.IgnoreCase);
    int i = 0;
    result = Regex.Replace(result, @"(\?)", m => "@" + (i++).ToString());
    return result;
}

static void Main(string[] args)
{
    string input = "Code = ? And Desc = ? Or Qty = ?";
    Console.WriteLine("{0} --> {1}", input, Translate(input));
}

You may of course try to merge all into one regex but that becomes quite messy.
Cheers
Andi