How to clean invalid SPWebConfigModifications

For future reference (after I hit my head on the wall for 3 days):

You can use this tool:

http://ianankers.wordpress.com/2011/07/14/web-config-modification-manager-for-sharepoint-2010/

It will display all the mods for each WebApp installed in your farm, you can add new ones and delete old ones.

webapp, , script :

using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using Microsoft.SharePoint;
using Microsoft.SharePoint.Navigation;
using Microsoft.SharePoint.Administration;

namespace ModTool
{
    class Program
    {
        static void Main(string[] args)
        {

            SPSite site = new SPSite(args[0]);
            SPWebService service = site.WebApplication.Farm.Services.GetValue<SPWebService>();


            if (args.Length == 1 || string.IsNullOrEmpty(args[1]))
            {
                Console.Out.WriteLine("Listing all Mods and Owners");
                foreach (SPWebConfigModification mod in service.WebConfigModifications)
                {
                    Console.Out.WriteLine("Mod:" + mod.Name + ", Owner:" + mod.Owner);
                }
            }
            else
            {
                Console.Out.WriteLine("Removing all mods owner:" + args[1] + ", reference site:" + args[0]);

                List<SPWebConfigModification> toDelete = new List<SPWebConfigModification>();

                foreach (SPWebConfigModification mod in service.WebConfigModifications)
                {
                    if (mod.Owner == args[1])
                    {
                        toDelete.Add(mod);
                    }
                }

                Console.Out.WriteLine("Found " + toDelete.Count + "Mods");



                foreach (SPWebConfigModification mod in toDelete)
                {
                    service.WebConfigModifications.Remove(mod);
                }
                service.Update();
                SPWebService.ContentService.ApplyWebConfigModifications();
                Console.Out.WriteLine("Done!!");
            }
        }
    }
}

:

ModTool http://site - List all the mods for the farm, site is just an entry point
ModTool http://site owner -Deletes all the mods for the far wich owner is "owner"