I think you’re stuck with what C# gives you, and getting errors suggests a poorly implemented UrlDecode function on the other end.
With that said, you should just need to loop through the string and uppercase only the two characters following a % sign. That’ll keep your base64 data intact while massaging the encoded characters into the right format:
public static string UpperCaseUrlEncode(string s)
{
char[] temp = HttpUtility.UrlEncode(s).ToCharArray();
for (int i = 0; i < temp.Length - 2; i++)
{
if (temp[i] == '%')
{
temp[i + 1] = char.ToUpper(temp[i + 1]);
temp[i + 2] = char.ToUpper(temp[i + 2]);
}
}
return new string(temp);
}