VAT is incredibly complicated, and you should always seek advice about the VAT treatment of any transaction if you are unsure. Bear in mind that VAT is calculated on turnover, not profits, so it comes off the top line and any mistakes are potentially costly.
Generally, HMRC favours pro-active behaviour when it comes to rectifying errors – for example, HMRC can charge you a penalty of up to 100% of any tax under-stated or over-claimed if you send a return that contains a careless or deliberate inaccuracy so there is a real focus on behaviours and genuine errors will ordinarily be resolved.