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)
{
document.Load(fileName);
Console.WriteLine(fileName);
}
}