"but apparently not ' could be used as a subordinate clause after a main clause that represents an uncertain statement,something that can not be established accurately as a fact, but seems to be so.It is used then to conclude that the uncertain statement is obviously unreliable and not to be depended upon. Example: "He thinks he is qualified enough for the post, but apparently not." The main clause here represents the uncertainty of him being qualified ( he thinks). The second clause 'but apparently not' ,decides that it is obviously not the case.