Dim f_adresse As String = System.AppDomain.CurrentDomain.BaseDirectory
Dim f_temp As String = f_adresse & "TEMP\"
Dim f_fichier As String = "20381235051-01-FF12-03.xml"
Dim f_certificat As String = f_adresse & "aG9CcVpHVndCWTd3WlVOVw==.p12"
Dim f_pwd As String = "GiQ5uTsBZ9gHxzNH"

Dim xmlFile As String = f_temp & f_fichier
Dim MonCertificat As X509Certificate2 = New X509Certificate2(f_certificat, f_pwd)

Dim xmlDoc As XmlDocument = New XmlDocument()
xmlDoc.PreserveWhitespace = True
xmlDoc.Load(xmlFile)

Dim signedXml As SignedXml = New SignedXml(xmlDoc)
signedXml.SigningKey = MonCertificat.PrivateKey
Dim KeyInfo As KeyInfo = New KeyInfo()
Dim Reference As Reference = New Reference()
Reference.Uri = ""

Reference.AddTransform(New XmlDsigEnvelopedSignatureTransform("true"))

signedXml.AddReference(Reference)

Dim X509Chain As X509Chain = New X509Chain()
X509Chain.Build(MonCertificat)

Dim local_element As X509ChainElement = X509Chain.ChainElements(0)
Dim x509Data As KeyInfoX509Data = New KeyInfoX509Data(local_element.Certificate)
Dim subjectName As String = local_element.Certificate.Subject

x509Data.AddSubjectName(subjectName)
KeyInfo.AddClause(x509Data)

signedXml.KeyInfo = KeyInfo
signedXml.ComputeSignature()

Dim signature As XmlElement = signedXml.GetXml()

signature.Prefix = "ds"
signedXml.ComputeSignature()
signature.ChildNodes(0).Prefix = "ds" 'this line breaks my signature
signedXml.ComputeSignature()

For Each node As XmlNode In signature.SelectNodes("descendant-or-self::*[namespace-uri()='http://www.w3.org/2000/09/xmldsig#']")
    If node.LocalName = "Signature" Then
        Dim newAttribute As XmlAttribute = xmlDoc.CreateAttribute("Id")
        newAttribute.Value = "SignatureSP"
        node.Attributes.Append(newAttribute)
    End If
Next node

Dim nsMgr As XmlNamespaceManager
nsMgr = New XmlNamespaceManager(xmlDoc.NameTable)
nsMgr.AddNamespace("sac", "urn:sunat:names:specification:ubl:peru:schema:xsd:SunatAggregateComponents-1")
nsMgr.AddNamespace("ccts", "urn:un:unece:uncefact:documentation:2")
nsMgr.AddNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance")
nsMgr.AddNamespace("tns", "urn:oasis:names:specification:ubl:schema:xsd:Invoice-2")
nsMgr.AddNamespace("cac", "urn:oasis:names:specification:ubl:schema:xsd:CommonAggregateComponents-2")
nsMgr.AddNamespace("udt", "urn:un:unece:uncefact:data:specification:UnqualifiedDataTypesSchemaModule:2")
nsMgr.AddNamespace("ext", "urn:oasis:names:specification:ubl:schema:xsd:CommonExtensionComponents-2")
nsMgr.AddNamespace("qdt", "urn:oasis:names:specification:ubl:schema:xsd:QualifiedDatatypes-2")
nsMgr.AddNamespace("cbc", "urn:oasis:names:specification:ubl:schema:xsd:CommonBasicComponents-2")
nsMgr.AddNamespace("ds", "http://www.w3.org/2000/09/xmldsig#")

xmlDoc.SelectSingleNode("/tns:Invoice/ext:UBLExtensions/ext:UBLExtension[2]/ext:ExtensionContent", nsMgr).AppendChild(xmlDoc.ImportNode(signature, True))
xmlDoc.Save(xmlFile)

'check the signature
Dim nodeList As XmlNodeList = xmlDoc.GetElementsByTagName("ds:Signature")
If nodeList.Count <= 0 Then
     MsgBox("Verification failed: No Signature was found in the document.")
     Exit Sub
End If

If nodeList.Count >= 2 Then
     MsgBox("Verification failed: More that one signature was found for the document.")
     Exit Sub
End If
signedXml.LoadXml(CType(nodeList(0), XmlElement))
msgbox("Check Signature : " & signedXml.CheckSignature())