• Retiremental benifits hold-conditional acceptance of resignation

I was working as a jr.civil engineer in A.P.M.C. (a semi govt.public body establishment) and I offered my resignation letter on 01/08/15 with  one months notice.
Prior to this some outsiders have made some allegations and charges on me by application. So my immediate employer referred it to next higher authorities to do the needful. In all this matter i was not  intimated nor written. Uptil Then and upto acceptance of resignation my authorities did not informed me about any enquiry only mentioned in reference letter which was issued to me on the last date of notice period that i accepted
i had my duties for 31 years in this establishment but due to heavy politics and feeling injustice(no promotion-no up gradation of pays still guiding and ordering by main authority for pay fixation –entered in high court w.p.)  to me i offered my resignation. After completion of one months notice period my employer asked me to continue for one more month as they have asked for directions regarding charges implanted by outsiders. so i continued 01/10/15.In the board meeting of 05/10/15 they sanctioned my resignation letter with conditions that any outcome of enquiry will be binding on me i.e. conditionally  accepted my resignation.
My wife is having her own proprietory unregistered service establishment of cad drawings, estimation,planning. She is electrical engineer by education but by employing private civil engineers she is working as a contractor and offering services.My office establishment also hired her service since 1999-2006 and paid certain amount against services provided by her firm.These payments were paid by employer after receival of official bill,and with board meetings confirmation.
But  in audit memo there were adverse remarks about hiring services and payment of service charges.As she is my wife.But i was  not deciding power no clarification uptil  today has been saught from me against audit memo.
My office rivals/competitors intentionally made its issue and shaking hands with local newspaper reporters started posting defaming news in bold headings.  
Now enquiry officer in its findings placed charges stating that payments made to my wife’s firm is illegal and for that  i should reimburse all the payments paid to my wifes proprietory unregistered office since 1999-2006 and Denying my P.F./Gratuity and retirement benifits. E.O.never wrote or intimated me that its your enquiry is going on and also never asked for my clarification.
After acceptance I wrote my Ex-authorities/E.O. that As my resignation is accepted Enquiry can’t be conducted as there is no relation of employer and employee left( accepted resignation on 5th oct 2015 and called my wife for clarification on28th oct2015)
My P.F.and gratuity,leave encashment amount is with my office itself.This total amount is 4 times more than whatever claim made by E.O. in its findings.My office is not having any pension facility so this is the only source of income for survival after retirement. After acceptance they not conveyed me any sort notice nor they answered my claim letters for gratuity and p.f. notice.I have entered in to labour court for gratuity and entering in civil court for p.f. and other benefits.But it is going to take about 2-3 years.  Kindly guide .