Last night Mr Naughton's sister said she had not known the correct way of getting the letters to the court, and that was where the confusion arose.
She posted the letters to the judge. They were returned unopened to her in court yesterday.
She believed the contents of the letters would definitely have influenced the outcome of the case.
Ms Naughton said she would sell the letters to the media on condition that they were reprinted in full.
Several newspapers were interested in buying the letters, she said, and negotiations were ongoing last night.
She said she was being "hounded" for the letters and could not return to Galway.
(The Irish Times does not buy material in these circumstances.)
Ms Naughton, who asked that her first name be concealed, said she had grown up in a large family.
She had never experienced "any animosity or interference" from Patrick Naughton.
She said her brother was a good person and a lovely and helpful brother.
"I still believe in his innocence," she said.
She added that his appeal would prove his innocence.
"I'm sure that the truth will come out in the end."