David McNamara fathered the child with Socci.
Prosecutors say he strangled Socci in June of 2011 and then left her body along a nature trail on the outskirts of Auburn.
McNamara claims he is innocent. The original murder indictment handed up against him was thrown out because McNamara was not allowed to testify before the grand jury.
Socci's father tells CNYcentral that McNamara was trying to get visitation rights with Sydney, while he's in jail.
McNamara is behind bars on unrelated prescription drug charges.
The judge denied the visitation request.
Prosecutors are trying to re-indict McNamara on murder charges. Katie Socci's parents are raising their granddaughter.