I found out how to find this file with wrong encoding. I've written simple C# program that uses the same method that CI seems to be using (by looking at stacktrace). It broke just on the corrupted file and I could see it's location.
static void Main(string args)
var path = @"path_to_your_app_data\CIRepository";
string filenames = Directory.GetFiles(path, "*.xml", SearchOption.AllDirectories);
var document = new XmlDocument();
foreach (var fileName in filenames)