The best-case scenario will result in the case officer accepting that the projects detailed in your claim are eligible under the R&D guidelines, resulting in the total amount of qualifying expenditure that was submitted being approved. In the worst case, the projects will be deemed to not be eligible, even after appeal. In those cases, none of the qualifying expenditure will be approved and the Inspector will be required to consider penalties for careless or inaccurate submission of tax returns.
Our experience varies on a case by case basis, and the result is dependent on the underlying quality of work put forward. Where clients have submitted a claim to HMRC in good faith, even if the Inspector concludes against allowing the claim, our experience is that we can work with HMRC to agree a way forward that does not result in the payment of penalties, provided that the claimant commits to understanding and abiding by HMRC guidance going forward.