Rectification request rejected by IT department

An employee, who is entitled to relief under Section 89, is required to submit Form 10E.

It has to be filed online at the e-filing portal and has to be filed before filing of the Income Tax Return

Since you failed to file 10E , 89 Relief has been disallowed.

And this may fall within the scope of rectification under 154 but it is at discretion of the AO

Better you accept your error of non-filing 10E in in time and pay tax and close the chapter.

1. Rectification request u/s 154 can be made for the following,
i) an error of fact,
ii) an arithmetic mistake, 
iii) a small clerical error,
iv) an error due to overlooking compulsory provision of law
2. The above mistake may fall under (iv) above as form 10E is a compulsory document that needs to be produced and has not been done at the time of filing the original return. 
3. As as far my opinion, if it is a genuine mistake on part of you, then the rectification request should be honored and accepted your form 10E (provided it is correct) and pass an order accordingly. 
4. Because only for these mistakes rectification request u/s 154 have been brought in and not to unnecessarily burden the taxpayer for his/her genuine mistake. 
Please correct me if the above solution has an alternative view. 

It was a genuine mistake realized later which was tried to be rectified by filing rectification under section 154 along with form 10E.

However the same has been rejected by the department with following remarks

"On Verification, it is seen that there is no prima facie error in the order which you have sought to be rectified. There fore, your
application for Rectification under Sec.154 is rejected, for the following reasons(if any)" 

Your Rectification Application cannot be processed for your ITR Form Type. We regret to inform you that your application for
rectification could not be processed at this point of time because a Suomotto rectification for the mentioned PAN-AY is in-progress/
completed at CPC. You may apply for re-rectification again only after an Order in respect of the above is issued. Please note that an Application for re-Rectification, if required by you, will have to be made again, in respect of the latest order for the relevant Assessment Year.

Now what should we do as the refund is of high amount. Instead of refund department has issued demand notice along with intimation order u/s 143(1) against original ITR.

Thanks.