As a follow-up. Would send both sets of slides to an expert pathologist as these "suspicious" changes can be seen in Hashimoto's and are often benign.
Unfortunately, we sometimes need surgery to make a definite diagnosis. If it is mild atypia and not highly suspicious on cytology, then the Afirma test can be helpful if surgery is not otherwise indicated/desired. If it is highly suspicious, then the Asuragen Thyroid miRInform test can help determine the extent of surgery.
Sounds suspicious, but sometimes having another pathologist take a look can be helpful