The ruling made has nothing to do with VAT. Its to do with the benefit in kind rules.
By the look of your post you have a Caravelle and as such this would never have been classed as a van and the VAT reclaimable, unless it was 100% business use and for the purpose of the trade.
As for BIK, the benefit in kind on a VW Caravelle is circa £18k meaning personal tax due of around £3.6K (20%) ir £7.3K (40%). As well as Class 1a National Insurance paid by the company of £2.5K.
A £39K Kombi if classed as a van would have a BIK of £3,230 so around £646 (20%) or £1,292 (40%) the same vehicle classified as a car would have a BIK of £14,659 and £2,932 (20%) or £5,863 (40%). This is a large jump. But an even bigger increase and one that most forget about , is if fuel is paid for by the company as this could result in a fuel benefit of £8,362 and additional tax of £1,672 (20%) or £3,345 (40%) compared to a van fuel charge of only £610 and tax of £122 (20%) or £244 (40%).
In summary the same Kombi could have a charge under the old rules of £768 (20%) - £1,536 (40%) to a stonking £4,604 (20%) - £9,208 (40%) plus the associated class 1a national insurance contributions paid by the company.