One of sale deed in title chain is missing

You can issue a legal notice to the seller to hand over the chain document failing which you can file a suit for recovery 

Can I lodge fir for certified copy behalf of seller or it becomes problematic .

I want to sell property immediately

Any other options available to avoid suit

You know the numbers of the previous documents, apply for certified copies of the documents in the sub registrar office.

Yes I know the number but for loan process bank asked for fir and notice in two paper

How I can register fir for document which are in someone's ( seller ) custody

Whether the bank want previous documents or a complain copy?

You cannot give a complaint for the documents which were actually not lost by you.

You can ask your vendor to produce the same by issuing a legal notice