Hola Micke
Yo lo tengo tal cual, o por lo menos, tengo todos los nodos que comentas pero sigo teniendo el inconveniente.
<?xml version="1.0" encoding="UTF-8"?>
<NominaIndividual xmlns="dian:gov:co:facturaelectronica:NominaIndividual" xmlns:ds="
http://www.w3.org/2000/09/xmldsig#" xmlns:ext="urn:oasis:names:specification:ubl:schema:xsd:CommonExtensionComponents-2" xmlns:xades="
http://uri.etsi.org/01903/v1.3.2#" xmlns:xades141="
http://uri.etsi.org/01903/v1.4.1#" xmlns:xs="
http://www.w3.org/2001/XMLSchema-instance" xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance" SchemaLocation="" xsi:schemaLocation="dian:gov:co:facturaelectronica:NominaIndividual NominaIndividualElectronicaXSD.xsd">
<ext:UBLExtensions>
<ext:UBLExtension>
<ext:ExtensionContent>
<ds:Signature Id="Signature-6e765a00d88e2222380c4d663192bb3e610ab3baf78567fbe2c6489ad4b5e217cb6bb7858657c15bdac79a41c671ad15">
<ds:SignedInfo>
<ds:CanonicalizationMethod Algorithm="
http://www.w3.org/TR/2001/REC-xml-c14n-20010315" />
<ds:SignatureMethod Algorithm="
http://www.w3.org/2001/04/xmldsig-more#rsa-sha256" />
<ds:Reference Id="Reference-6e765a00d88e2222380c4d663192bb3e610ab3baf78567fbe2c6489ad4b5e217cb6bb7858657c15bdac79a41c671ad15" URI="">
<ds:Transforms>
<ds:Transform Algorithm="
http://www.w3.org/2000/09/xmldsig#enveloped-signature" />
</ds:Transforms>
<ds:DigestMethod Algorithm="
http://www.w3.org/2001/04/xmlenc#sha256" />
<ds:DigestValue>SIGNATURE_VALUE</ds:DigestValue>
</ds:Reference>
<ds:Reference URI="#Signature-6e765a00d88e2222380c4d663192bb3e610ab3baf78567fbe2c6489ad4b5e217cb6bb7858657c15bdac79a41c671ad15-KeyInfo">
<ds:DigestMethod Algorithm="
http://www.w3.org/2001/04/xmlenc#sha256" />
<ds:DigestValue>rPNBWVGYUwlIXHlrgMB2Qik2Rzu8YMdFuOzHN1dDLaQ=</ds:DigestValue>
</ds:Reference>
<ds:Reference Type="
http://uri.etsi.org/01903#SignedProperties" URI="#xmldsig-Signature-6e765a00d88e2222380c4d663192bb3e610ab3baf78567fbe2c6489ad4b5e217cb6bb7858657c15bdac79a41c671ad15-signedprops">
<ds:DigestMethod Algorithm="
http://www.w3.org/2001/04/xmlenc#sha256" />
<ds:DigestValue>0ugy49zC5gC1Jkox8XPutlILLTnNe6olfph01jy96IY=</ds:DigestValue>
</ds:Reference>
</ds:SignedInfo>
<ds:SignatureValue>HGqX3KlhPGModerSccst/ZS8OzcvQid8WGa35tz/8V9v4yY4AON3PNcRSOG+V2IQ8lOl7WLzXwwRFREGG782x3WbFAHGVsrIgOb4rJapQQWvZ5v8rWxVK31ZuyyIRPZP+tLsustG7AGfm2oXRN+oAXY0dTiM6zZtvtYN5OR5qRLqQxEppsyJmXXyfV1CkP5yzSmMxzIPjNjdw7v/wmCOLhEIdkfaeoOVoW8ARBWjfIlGpyeJUODUbJQIolE0aYiyiiREDIg3feZwD3zmde5132BaOo7c1Vq5ySYjWcofkHVJd8r15NiLDiEIq2HQMNooFjFaSxBgL6310fvz2z2vQg==</ds:SignatureValue>
<ds:KeyInfo Id="Signature-6e765a00d88e2222380c4d663192bb3e610ab3baf78567fbe2c6489ad4b5e217cb6bb7858657c15bdac79a41c671ad15-KeyInfo">
<ds:X509Data>
<ds:X509Certificate>CERTIFICATE_DATA</ds:X509Certificate>
</ds:X509Data>
</ds:KeyInfo>
<ds:Object>
<xades:QualifyingProperties Target="#Signature-6e765a00d88e2222380c4d663192bb3e610ab3baf78567fbe2c6489ad4b5e217cb6bb7858657c15bdac79a41c671ad15">
<xades:SignedProperties Id="xmldsig-Signature-6e765a00d88e2222380c4d663192bb3e610ab3baf78567fbe2c6489ad4b5e217cb6bb7858657c15bdac79a41c671ad15-signedprops">
<xades:SignedSignatureProperties>
<xades:SigningTime>2021-11-02T10:42:37.841-05:00</xades:SigningTime>
<xades:SigningCertificate>
<xades:Cert>
<xades:CertDigest>
<ds:DigestMethod Algorithm="
http://www.w3.org/2001/04/xmlenc#sha256" />
<ds:DigestValue>U6hjxxYP8tUJQrydfoE9p9Vxaw8lhwzq945T+rySPB0=</ds:DigestValue>
</xades:CertDigest>
<xades:IssuerSerial>
<ds:X509IssuerName>ISSUER_NAME</ds:X509IssuerName>
<ds:X509SerialNumber>SERIAL_NUMBERC</ds:X509SerialNumber>
</xades:IssuerSerial>
</xades:Cert>
</xades:SigningCertificate>
<xades:SignaturePolicyIdentifier>
<xades:SignaturePolicyId>
<xades:SigPolicyId>
<xades:Identifier>
https://facturaelectronica.dian.gov.co/politicadefirma/v2/politicadefirmav2.pdf</xades:Identifier>
<xades:Description>Política de firma para facturas electrónicas de la República de Colombia</xades:Description>
</xades:SigPolicyId>
<xades:SigPolicyHash>
<ds:DigestMethod Algorithm="
http://www.w3.org/2001/04/xmlenc#sha256" />
<ds:DigestValue>dMoMvtcG5aIzgYo0tIsSQeVJBDnUnfSOfBpxXrmor0Y=</ds:DigestValue>
</xades:SigPolicyHash>
</xades:SignaturePolicyId>
</xades:SignaturePolicyIdentifier>
<xades:SignerRole>
<xades:ClaimedRoles>
<xades:ClaimedRole>supplier</xades:ClaimedRole>
</xades:ClaimedRoles>
</xades:SignerRole>
</xades:SignedSignatureProperties>
</xades:SignedProperties>
</xades:QualifyingProperties>
</ds:Object>
</ds:Signature>
</ext:ExtensionContent>
</ext:UBLExtension>
</ext:UBLExtensions>
</NominaIndividual>