We punctuate a fragment the same way that we punctuate the complete sentence it stands for. This is simply the way the language works.
...A With John. He had been ill.
...A I stayed with John. He had been ill.
...I have. It has been a long time, however.
...I have seen it. It has been a long time, however.
It follows, then, that this is also correct punctuation.
...You were alone at the time; is that correct?
...You were alone at the time; correct?
...Mr. Johnson had been fired; is that right?
...Mr. Johnson had been fired; right?
There is no justification for putting a comma instead of the semicolon here. It creates a run-on sentence.
Happy punctuating!
Margie