There seems to be inherent problems in the client's accounts. That is to say, his P/L does not match with his books of accounts (sales register). This is in violation of all basic tenets as the Financial Statement is not reflecting a true and fair view of the accounts (from accounting & auditing POV, Income tax POV and also GST POV) and will land the client (even the auditor) in big problems.
Nevertheless, if SCN is issued by the Department at this stage, it is still defendable in my opinion. The Department cannot simply tax the amount shown as "adjustments in turnover due to reasons not listed above", without establishing first that such amount is "consideration for supply". Consequently, Time of supply, Place of supply, classification, etc... also have to be established qua the supply and without which, the SCN will be vague and will not sustain.
That being said, since the P/L does not reflect a true and fair view of the accounts, the Department can carry out Audit, Special Audit, inquiry/ investigation etc in their powers to ascertain the true picture and raise demands accordingly.