This isn't really a question that can be answered generically via an internet forum, as everything will depend on the facts! A few general points can be made, though.
HMRC has yet to prove its point on PAYE and NICs being due on EBT arrangements, as it lost its challenge to the Rangers FC EBT & loan schemes at both FTT and UT in Murray Group Holdings. Murray has now gone into liquidation, so HMRC's appeal to the Court of Session will probably need to wait for another case.
However, if the scheme in question had a DOTAS number, HMRC is likely to issue APNs, with money payable on account whether or not HMRC is ultimately found to be right. It has been delaying the issue of APNs on EBT schemes because, although the tax legislation was passed in 2014, the parallel NIC legislation only took effect on 12 April, and it wanted to collect both alleged PAYE and NIC arrears together. It has, however, issued some APNs to recover any claimed CT relief for contributions, a point that it has established by arguing that, tax relief being one of the main purposes of entering into the scheme, the expenditure had a duality of purpose that was sufficient to disqualify any CT relief. The contributions were argued not to have been made wholly and exclusively for the purposes of the trade, and both FTT and UT have agreed so far (Google "Scotts Atlantic Management").
There is a debate about what you do in your accounts if you have used a scheme and are expecting, but haven't yet received, an APN, but that is also well beyond the scope of a forum post.
If the client wants to concede rather than fight HMRC's arguments, he has missed the deadline for the EBT settlement opportunity, which required registration by 31 March, but HMRC won't turn down the offer of the appropriate amount of money. There is no longer a standardised deal on the table, but they are always open to offers in settlement (and it remains to be seen, but the amount they seek probably hasn't changed since 31 March). Some businesses have settled because they want to wipe the slate clean and move on, some need a clean slate before they can sell their business, and some are hanging on in the hope that somebody else will win the argument, but the APN regime has changed the economics of hanging on.