Absolutely not. The warranty is designed to protect you from poor workmanship by the builder. However, they might try to blame any issues you discover during your snagging period on your loft flooring.
But in our experience, showing them that LoftZone has a BBA Certificate and has been fitted by an authorised installer will make them look for the real source of the problem and get it resolved. Additionally, the market leader NHBC has confirmed that using our raised loft boarding system does not affect their warranty.