The assesee or its representative should approach their respective designated authority. In case no response  is received one may approach the High Court by filing writ petition .

If the CIT (A) has passed the ex parte order without giving an opportunity of hearing , the assessee should file an  rectification application before the CIT(A) to rectify the order . The assessee can also file an appeal to Tribunal on the grounds of violation of principle of natural justice and make an application for an early hearing of appeal .If the Tribunal set aside the appeal to CIT (A) to decide the appeal on merits giving an opportunity of hearing the assessee  can avail the benefit of the scheme.  One has to consider whether the  assessee has given an intimation to the CIT (A) in writing that the assessee  is desirous of  availing the benefit of the scheme still the  order was passed by the CIT (A) one may approach the High Court by  way of writ petition . 

The date of filing & beneficial payment under VSVA was extended to June 30, 2020 vide Finance Ministry issues Taxation and other Laws (Relaxation of Certain Provisions) Ordinance, 2020 dated March 24, 2020; However, as per the press release dated May 13, 2020, the extension to of beneficial payment is extended to December 31, 2020. As  the scheme it self is extended till 31 -12 -2020 , the date of filing Form 1 is also extended . We are expecting one more ordinance or Clarification from the Board .

Please contact the designated authority , they will clarify . Many such difficulties are faced by the assesses the authorities may rectify the mistake or may issue the clarification at the earliest.

As we understand, the assessee fulfils all the criteria to be eligible under VSVA. Section 9 of VSVA is an exhaustive list to whom the Act shall not apply. As the case of the assesee does not fall under any of the criterion under section 9 of VSVA.  The assessee can avail the benefit of the scheme .  

If the ITAT has set aside the matter to CIT (A) to decide the matter on merit  the  appeal is pending as on the specified date.ie 31-1-2020 . If the appeal is set a side to the AO , it is desirable to file an Miscellaneous application before the Tribunal and pray for recalling of the order. The miscellaneous application can be filed with in six months  of the receipt of the order. In  Devendra G.Pasale v ACIT ( 2010) 333 ITR 263 (Guj) (HC) has held that even ex parte order passed on merits can be set aside as per Rule 24 of the ITAT Rules  also refer, . Lalitnirman Business Development (P.) Ltd v ITO  (2018) 259 Taxman 23 (Bom) (HC)

It is desirable to  file an appeal before the Appellate Tribunal with condonation of delay . Request the Honourable vice president to fix the appeal for hearing only on condonation of delay. Once the delay is condoned it relates back  and the assessee  can avail the benefit of the VSVA. 

There is no clarification for cases where deemed appeal is not filed. However, going by the language of VSVA strictly; The case is eligible for VSVA and there is no express language dictating otherwise. However , it is desirable to file an appeal now with application for condonation of delay. The assesses should request the CIT(A) to pass the order on condonation of delay . Once the delay is condoned appeal relates back , hence the assessee will be eligible to avail the benefit of VSVA .

Yes you nay revise the form before issue of certificate by Designated authority . Representation is sent to CBDT to clarify at what circumstances the assessee can  revise the form We are expecting clarification from CBDT on this particular issue .

From what we understand from your query, if your case holds merits its better to contest the matter on merits. Further, under the VSVA, if the payment is made before December 31, 2020, you will have to pay only the disputed tax amount; the interest would be waved. However, if the addition is for the AY 2017-18 and it is at the special rate as per section 115 BBE of the Income tax Act, 1961, there will be no relief to that effect. If you are able to substantiate the source of investments by filing additional evidence it may be worth contesting in appeal . It may be desirable to take specific grounds  on natural  justice and file an affidavit why could not attend before the A0 and pray  for admitting additional evidence .