Important:
This answer is based on tax law year ending 28 February 2021.
Answer:
From the information supplied it would appear that the previous bookkeeper submitted a single VAT return for the entire year. We are not sure what happened to the other returns. The best way out of this would be to compute the correct VAT liability for each tax period reflecting input and output tax and submit the corrected returns. If all the VAT returns had been submitted previously, you would need to object to each return and request SARS to condone the late submission of the objections. You can also consider the Voluntary Disclosure route provided that the net result is not a refund due by SARS. There is no way to guarantee that SARS would not do an audit. The best way would be to “come clean” and ensure that proper processes are put in place to avoid a similar occurrence in the future.