In case if the company did not accept the resignation you serving the notice period is meaningless .
Did thay raise objections to you after you tendered the resignation while still in service ?
In case of no reply from the employer, it could be deemed acceptance .
As per Indian Laws no employer can force you to work for them against your will. You are under no obligation to complete the pending work after you submitted the resignation and served notice period.
The company should have made arrangements for your replacement by handover and handholding of another person . The loss incurred fully attributable to themselves.
Have they given you any rationale for holding back your due salary and F&F ?
You should reply to the company's notice with your claims for due salary, F&F etc to maintain pressure for your dues and thwart any legal action .
I presume you have all relevant communications on record .