gistfile1.cs

void Main()
{
  var file = @"C:\Users\Me\Desktop\Certificates.txt";
  var a = JObject.Parse(File.ReadAllText(file));
	var cert = a["Certificates"][0];
	
	// Get the UIDs for the existing boards and circuits.
	var boards = cert["Boards"].Select (x => (Guid)x["UniqueId"]).ToArray();
	var circuits = cert["Boards"].SelectMany (x => x["Circuits"]).Select (x => (Guid)x["UniqueId"]).ToArray();
	
	var changes = new List<string>();
	foreach (var board in cert["Boards"])
	{
	    var designation = (string)board["Designation"];
	    var supplyBoard = (Guid)board["SupplyBoard"];
	    var supplyCircuit = (Guid)board["SupplyCircuit"];
		
		if (supplyBoard != Guid.Empty && !boards.Contains(supplyBoard))
		{
		    board["SupplyBoard"] = Guid.Empty;
			  board["SupplyIsOriginOfInstallation"] = true;
			  changes.Add("Set supply to origin for " + designation);
		}
    
		if (supplyCircuit != Guid.Empty && !circuits.Contains(supplyCircuit))
		{
		    board["SupplyCircuit"] = Guid.Empty;
			  board["SupplyIsOriginOfInstallation"] = true;
			  changes.Add("Set supply to origin for " + designation);
		}
	}
  
	File.WriteAllText(file, a.ToString());
	changes.Dump("Changes");
}