...in my case HMRC wanted a detailed business plan showing how the company could become profitable and when.
To which you might have answered that all this flight training, with the aim of becoming a commercial pilot, was part of boosting the companies revenue stream in the medium term and forms part of a change in the strategy of the business since inception etc, etc blah..??
There is a lot made of accounting fees, answering to HMRC and the fear of penalty. Frankly if you have a real business with a plan that is aviation centred then there is nothing to worry about because there are a great many real reasons why one might embark on pilot training to enhance/support or even evolve a current business.
For instance one great and long running aviation business in the UK would be Martin Baker. No doubt at some point, having done all the boffin bits, it might have been useful for someone to actually fly a plane and test it. Sure you could hire a pilot/plane short term but it would be perfectly reasonable for them to have trained someone to fly to support the needs of the business in the long term, and no doubt expensed via the business which included reclaiming the VAT.
On a smaller scale what about someone that might do aircraft re-sprays? Perhaps learning to fly might enable the business to give better service, etc, etc.
Business can change direction and evolve there is nothing dodge in that.