Hello and thank you for your question.
Step 1 is to make sure they have been underpaying. In other words, are the things you are asserting might be taxable really taxable?
Step 2 is to file amended returns.
Step 3 is to set up a payment plan for the unpaid balance if your client can't pay it immediately (you can generally get power of attorney and do this for your client if you like).
Obviously, they'll want to file correctly going forward too. Whether it triggers suspicion is irrelevant.
Your question is what options are available, but there really aren't any... Your client can elect to not correct the prior returns and run the risk as the case may be. That is up to your client, but it seems like a case where you would recommend amending. Your client can also choose to keep doing things incorrectly as the case may be. Again that is up to your client, noting that you cannot prepare and sign the returns with these substantial understatements if you determine that to be the case. You can simply offer to prepare them correctly or not at all.
Other than the above, I'm not sure what else to tell you, but if there is something else you want to discuss let us know. If I'm online I'll do my best to answer, or if not, then I would expect another expert here to help you in my place.