Notice period to be recovered by the company & relieving date confusion

Asking this question on my friends behalf. He works for an MNC and was asked (let's say on Jan 1st) to leave and three months (ends on March 31st) were given to find new opportunity. He was not asked by HR / line manager to raise any resignation request on system (i.e., SAP). He was informed verbally and through mail (post). Now, after three months (let's say on March 31st), he went to his office and raised resignation / exit request (as suggested by HR manager). However, when he raised resignation request on system, it auto-generated a releiving date which was three months from the day he raised resignation request. Let's say (for example) if Jan 1st was the day he was informed to leave then his last working day was March 31st. However, since he raised resignation request on March 31st, system auto-generated June 30th as his last working day (got extra three months). Nothing happened after this and my friend got salary for April and May. Now after 6 months he got NDF (No due form) from HR and they have mentioned March 31st as last working day. And, have mentioned 90 days as "notice period to be recovered". Important point is that from march till June they sent NDF 6-7 times and every time Jun 30th was mentioned as relieving date however, in the last NDF they sent, March 31st is given as last working day. Question: 1) what should be considered actual relieving date? March or June? 2) Does my friend need to pay anything to the company (two months salary)? 3) What if company demands and he doesn't pay? 4) what actions can company take here? Thanks in advance for your response..