Misguidance of IG for change of Directors of Pvt Ltd co

Industrial plot for a pvt ltd co was duly registrered and lease deed executed by then directors. In the course of time, Directors changed and Original Registered Lease deed of Co. was also lost by mistakenly. RIICO guided us for duplicate lease deed registration with new present directors as executants.Before presenting original papers to Sub registrar for registration we Consulted with IG if duplicate lease deed can be done in such situation.IG gave us a written order and directed Sub Registrar to registar duplicate lease deed for us.But when we presented originals to sub registrar, instead of duplicate lease deed they considered it as transfer of lease by way of assignment ( just for change of directors) and issued us a notice for stamp duty.Now the matter is pending in IG office.IG office said orally to us that they did not examined the papers properly and gave the previous order by mistakenly and now we are liable for stamp duty. We have not changed the name of the company only the previous directors resigned and new directors were been appointed in place.We have been misguided here by IG office!! . If duplicate deed was not possible we would have not presented papers to Sub registrar for execution.What can be done? Can the documents be rejected after issuing of receipt for duplicate lease deed?We are facing unnecessary monetary damage..please help and guide us.