It is very unusual for a transcript to be lost, but it can happen. The appellate court will demand an explanation from the court reporter. This may help your appeal. For further complaints about the court reporter, contact her state licensing association.
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Ms. Jaggers is quite correct that the record of what was said in a trial - what you are apparently calling a "transcript" - is rarely lost. BTW, the technical term for the record prepared by the court reporter is simply the "court reporter's record".
Over the years, several cases have been reversed and a new trial granted where through no fault of the defendant the court reporter's record was missing. However, as with most appeals law, the law on missing records is technical and complicated. So, my suggestion is that you sit down with a good APPELLATE criminal defense lawyer, and discuss what you set out here and get some advice specific to your situation.
Answers on Avvo are for general information purposes only and should not be relied upon as legal advice. No attorney / client relationship is created by providing this answer. For specific advice about your situation, you should consult a competent attorney of your choosing.