...

//подписанные атрибуты(SignedAttr)
final Attribute[] signAttrElem = info.signedAttrs.elements;

// *** проверка атрибута signing-certificateV2 ***

final Asn1ObjectIdentifier signingCertificateV2Oid = new Asn1ObjectIdentifier(
    (new OID(ALL_PKIX1Explicit88Values.id_aa_signingCertificateV2)).value);
Attribute signingCertificateV2Attr = null;

//получаем атрибут
for (int r = 0; r < signAttrElem.length; r++) {
    final Asn1ObjectIdentifier oid = signAttrElem[r].type;
    if (oid.equals(signingCertificateV2Oid)) {
        signingCertificateV2Attr = signAttrElem[r];
    } // if
} // for

if (signingCertificateV2Attr != null) {

    SigningCertificateV2 signingCertificateV2 = (SigningCertificateV2)
       signingCertificateV2Attr.values.elements[0];
    _SeqOfESSCertIDv2 essCertIDv2s = signingCertificateV2.certs;

    for (int s = 0; s < essCertIDv2s.elements.length; s++) {

        ESSCertIDv2 essCertIDv2 = essCertIDv2s.elements[s];

        CertHash expectedCertHash = essCertIDv2.certHash;
        AlgorithmIdentifier expectedHashAlgorithm = essCertIDv2.hashAlgorithm;

        IssuerSerial expectedIssuerSerial = essCertIDv2.issuerSerial;
        Asn1BerEncodeBuffer encodedExpectedIssuerSerial = new Asn1BerEncodeBuffer();
        expectedIssuerSerial.encode(encodedExpectedIssuerSerial);

        OID expectedHashAlgorithmOid = new OID(expectedHashAlgorithm.algorithm.value);
        CertHash actualCertHash = new CertHash(
            CMStools.digestm(cert.getEncoded(), expectedHashAlgorithmOid.toString()));

        ru.CryptoPro.JCP.ASN.PKIX1Explicit88.Certificate certificate =
            new ru.CryptoPro.JCP.ASN.PKIX1Explicit88.Certificate();
        Asn1BerDecodeBuffer decodeBuffer = new Asn1BerDecodeBuffer(cert.getEncoded());
         certificate.decode(decodeBuffer);

        GeneralName[] issuerName = new GeneralName[1];
        issuerName[0] = new GeneralName(GeneralName._DIRECTORYNAME,
            certificate.tbsCertificate.issuer);
        GeneralNames issuerNames = new GeneralNames(issuerName);

        IssuerSerial actualIssuerSerial = new IssuerSerial(issuerNames,
            certificate.tbsCertificate.serialNumber);
        Asn1BerEncodeBuffer encodedActualIssuerSerial = new Asn1BerEncodeBuffer();
        actualIssuerSerial.encode(encodedActualIssuerSerial);

        if ( !(Arrays.equals(actualCertHash.value, expectedCertHash.value) &&
            Arrays.equals(encodedActualIssuerSerial.getMsgCopy(),
            encodedActualIssuerSerial.getMsgCopy())) ) {

            System.out.println("Не тот сертификат, не выполняем проверку.");
            return false;
        } // if

    } // for

} // if

...

Collection<X509Certificate> chain = new ArrayList<X509Certificate>(); // список сертификатов
Collection<X509CertificateHolder> holderList = new ArrayList<X509CertificateHolder>();
...

for (X509Certificate cert : chain) {
    holderList.add(new X509CertificateHolder(cert.getEncoded()));
} // for

...
cadesSignature.setCertificateStore(new CollectionStore(holderList));