Civil dispute in supreme court

If the supreme court has passed an order closing the opportunity given to the respondent for filing their counter affidavit then they may not be permitted to file it again unless there's any exceptional and exclusive reason pleaded by them for not filing it on time.

However the respondent may be permitted to participate in the proceedings because they have already filed vakalatnama hence they can present their final arguments.

The discretion is totally with SC .it can allow or reject filing of counter affidavit of respondents. 

Yes.  It is the discretion of the SC to allow or reject the counter affidavit.

The matter is being listed before Registrar Supreme Court for comletion of pleading, isn't it?

Generally the Registrar gives 2 opportunities to the respondent(s), which can further be denied if objected by the petitioner / appellant.

However, there is no hard and fast rule as to how many opportunities shall be granted by the Court for filing counter affidavit.

What is the opinion and advise of the Sr Advocate / AoR / lawyer appointed by the petitioner / appellant in the instant case and what is your locus standi ??

Yes, the Supreme Court has absolute discretion. It is too hasty for this forum to give any suggestion.