The moment your father got arrested under the Prevention of Corruption Act,1988 in 2009, he would have been immediately placed under suspension under the State Civil Services (Discipline and Appeal)Rules and paid subsistence allowance at the admissible rate.
When he attained the age of superannuation after some time, he would not have been permitted to retire in view of the pending vigilance case; instead he would have been paid subsistence allowance at half the rate of his normal pension.
Whether he would get his pension and gratuity would be dependent upon the verdict of the criminal case instituted against him. If he is convicted, no terminal benefits.