If one underwent Judaism conversion and hold a conversion certificate with 3 Beit Din signature, the conversion is performed by an Orthodox Rabbi , but the Rabbi is not in the list of Israeli Supreme Court, is that person a Jew? If gentiles are not allowed to observe Shabbat, should the person keep Shabbat?
Yes that a person is jewish. The state of Israel has no halachik authority in determining who is a jew. If one converts with a valid orthodox conversion and bet din then one is a jew if the israeli rabbinate does not think so.