Confirmation received post Resignation

Hi , My probation period was 6 months. Post 6 months I received a auto mailer with HR signature stating my probation is extended by 3 months due to lack of documentation but my documents were provided by me before joining as well as for background verification for which I received a green signal . I had also showcased my original documents to my immediate manager & took signature on the Xerox copies which I uploaded in the HR portal multiple times but always received a system mailer that the documentation was incomplete. I then raised concern with the HR about the same. I got a reply stating if you have uploaded the documents & manager has approved in portal ignore the system.mailers. My manager was already marked in this mail but didn't respond. After all this I resigned since I received a better opportunity & since I was not confirmed employee my last working date in the system was after one month. I received a call from my manager that even though the system is showing 30 days of notice period I will have to serve 90 days since he had approved by confirmation but system rejected it. He also got the notice period updated in the system as 90 days post which he accepted my resignation. But I have not yet received the additional leaves as per the confirmed employee nor any confirmation letter. I raised this concern to higher HR manager but have not received any reply. In fact the manager & HR who changed the notice period in portal has told me that if I do not serve 90 days of notice period & donot upload the documents in system again , I will not receive reliving letter. Pleas suggest.