Occasionally you modify the web.config using the SPWebCongiModification class. Some times the config entries are not removed from the web.config. You can use the code below to exactly do this:
This is an exact copy of the code mentioend by Luis:
http://stackoverflow.com/questions/10732808/how-to-flush-invalid-spwebconfigmodifications
This is for my reference and I take no credit for this solution, 100% credit goes to Luis :)
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!!");
}
}
}
} Usuage: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 in the farm forwhich the owner is "owner" 
