Pardon my jumping in here - fascinating thread and a variety of positions....
I think the answer to the question posited above is "if you KNOW or SHOULD HAVE KNOWN that you were facilitating your client's fraud, you have liability - EVEN IF you explained to them that what they were doing was incorrect. Merely completing the form with data you KNOW or SHOULD HAVE KNOWN to be incorrect causes you to incur liability."
Now, keep in mind, if there is an honest disagreement, or a reasonable basis for doing what they are doing, an appropriate CYA may protect you - but if it clearly is not appropriate, then your facilitation of that act can be problematic.
PLUS, it'll ruin your reputation for being a "professional" at what you do.
Personally, I'd address it delicately with the client. A discussion around "pay is "comp" for plan purposes ONLY IF it's for work performed. "Hours" means hours ACTUALLY WORKED (or in some limited circumstances, that which you should have worked and been paid for), and the like. Depending on the circumstances, I'd even say to the client, "your accountant said..." and have a discussion about the merits of maintaining the plan as a tax qualified plan.
If all else fails, I'd probably fire the client (and I know, business is business, but you won't get many new clients if you let an existing client do something really really wrong.
Let me posit an extension of the hypothetical: Suppose you do nothing and the client get's audited and this is discovered, plan disqualified. Client talks to accoutnant, accountant say "I TOLD THE TPA - experts in the field, and they did NOTHING."
You think people might be looking to you for "malpractice" as "experts" in the field who knew something was amiss and didn't bring it to their attention?
By the way, under any scenario, the accountant is toast....