GSTR 9C - Peculiar Case of Two GST Registrations for a single entity. Need help

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There is an Partnership firm. The employees of the company by mistake applied the GST number in the name of the partner therefore on the portal the GST registration is in proprietor's name. Billing, upload of returns and GST Payment and ITC kept happening in the wrong Proprietorship Portal. After 6 months this was realized and then new GST Registration in the name of Partnership Firm was taken. For the remaining 6 months it was correctly uploaded and filed. While filing the tax audit, the entire turnover was naturally taken in the name of the partnership firm and filed. Now how do we file GSTR 9C as balance sheet would not be correct for either of the registrations since it was filed for 12 months in total combining both the portals turnover?

 

Facts of the case:

These are the facts of the case:

1. A partnership firm was formed in FY 18-19. Lets Call it ABC Firm.

2. Instead of taking the GST number in the name of the partnership firm, the employee took the GST registration in the name of the partner. Therefore on the GST portal the legal name is Mr.A but the trade name is ABC Firm.

3. The Sales upload, ITC etc all was taken and uploaded in Mr.A's GST registration portal for 6 months.

4. In the 7th month this mistake was realised and then a fresh GST registration was taken in the name of the firm and proper upload of invoice and ITC was done for the balance 6 months and is continuing now.

5. Since, the turnover technically belonged to the partnership firm, the Sales and Purchases were taken together for both these entities and consolidated to make the balance sheet, P&L etc of the ABC firm and the tax audit of the firm was completed based on this Balance Sheet for 18-19.

6. Now since the turnover exceeds Rs. 5 crores for both these entities in each of the respective 6 months, GST audit is applicable to both the registrations. 

7. But the issue is there is a consolidated balance sheet of ABC firm combining both these entities' turnover. The turnover shall not reconcile in either of the GST Registrations 9C. How do we report the same or suggestions on approach that can be taken in such a scenario?

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