I was suggesting claiming the full AIA because at £42,000 profit, there is more than enough to cover the £12,600 cost of the van. As @ian_roberts says, claiming AIA in full will reduce your taxable profit down to £29,400.
Claiming more than your available profit, would put you into the position of a taxable loss. While this can be carried forward to offset against future trading profits, it does waste the opportunity to utilise your full personal allowance during the year. This is assuming, of course, that you don’t have other income, e.g. salary, that already uses up your personal allowance.
So yes, if what you mean by it having a negative effect on your personal allowance is that you wouldn’t fully utilise it, you are correct.