Your father ws retired in the year 2006 and now we are entering into 2020, so what was he doing so for when he did not gt his retirement dues till date.

In any case the said criminal case is not 13 years old, hence there may be some other reason that your father is not getting his dues.

If your father is not involved in the criminal complaint case then he could have got it quashed through high court.

Now he can file a writ petition before high court seeking relief of his stopped terminal benefits.

for claiming the service dues your father can file a writ petition in the concerned High Court 

Observing that gratuity and pension are hard earned benefits of an employee and right to receive pension is in the nature of "property", the Supreme Court has held that this right cannot be taken away from a government employee pending departmental or criminal proceedings.

"It is an accepted position that gratuity and pension are not the bounties. An employee earns these benefits by dint of his long, continuous, faithful and un-blemished service. It is thus hard earned benefit which accrues to an employee and is in the nature of "property".

3) The court passed the judgement while dismissing the appeal of Jharkhand government against the state's high court order directing it to release the withheld dues of its retired employee Jitendra Kumar Srivastava, who had criminal cases pending against him.

4) file application before CAT against refusal to pay your father gratuity and pension 

1. Appeal against conviction under Section 498A is a statutory right, cannot be thrown out at the stage of admission if filed within limitation.

2. If father has also been convicted then during the pendency of appeal also his pension cannot be withheld. A writ petition can be filed in the High Court.

1. Except pension other retirement benefits can be withheld if he has been convicted. Mere filing of appeal does not operate as a stay on conviction. Unless conviction has been stayed by the court the retirement benefits can be put on hold.

2. That he was reinstated is now immaterial as he has been subsequently convicted. Department has not withheld his dues due to the fact that he was in JC, but because he has now been convicted after trial,

You can approach the appellate authority who has withhold the said benefits. The said conduct is not proper. He must be given at least a part of benefits in this case

Department cannot hold your father retirement benefits 

take legal proceedings before CAT for release of retirement benefits 

He has relief with CAT only for this also.

The department can conduct inquiry and dispose the same as per service regulations provided he has been charged with the irregularities connected with his service matters and not with the matrimonial disputes.

He has to initiate action as per law for recovering his terminal benefits.

When he is reinstated and than duly retired, retirement benefits cannot be withheld. Further employee’s pension or pensionary benefits cannot be withheld due to mere pendency of a criminal case.

Due to 48 hours JC, he can be suspended but pension benefits cannot be with held and on his reinstatement by order of CAT, this disability also wiped out.

File writ in HC.

1.  It is not clear wehther there is stay on his sentence or not.

2. if there is stay on his sentence then his retiral benefits can not be refused to be granted. 

he can file A writ petition before high court. 

The simple and best solution in this matter is filing a writ petition in HC as soon as possible.

1. You should file writ petition before High court for release of retirement benefits as he was reinstated by order of CAT and his dues which are not release are unconstitutional.

In The criminal appeal your father got acquitted. This fact must be brought to the notice of the department and adequate dues and pension based upin it must be demanded.

No the department cannot do anything like that. File an original application in CAT.