Dear Sir,
No need to worry about it.
Your auditor was right. He was not required to disclose the investment in shares but when you sale those shares, you have to show it in ITR for that year.
Don't worry if the investment is out of tax paid salary income then it's not an undisclosed income.
Capital gain is exempt on STT paid long term equity shares .
Please feel free to call/ revert in case of any doubts
Thanks and Regards
Abhishek Dugar
CA CS B.com