I doubt they would or can cancel an entire warranty for any modification unless they could show the alteration had effect upon the failure being warranteed. However, unless one had engineering-support for the alteration it would likely negate any owners claim against the mfr’r should a roll-over occur.
If lowering the ROPS is required to make the machine useful for your purposes, then I’d do it. If you truly are concerned about roll-over safety then I’d seek some mechanical engineering resource.
Roll overs occur through speed, cornering, driver inexperience, sub-standard road conditions, overloaded vehicles, fatigue, collision with another vehicle or object, or traversing a critical slope.
The other consideration you might encounter is “re-sale”. If you later sell the vehicle you may suffer loss-of-value due to the ROPS alteration unless you have engineering support and the alteration is performed accordingly. You might also think about liability to your guests, riders, and subsequent owners should you sell. (ALWAYS have any buyer sign an acceptance or buyers agreement that it is sold “As is, Where is, without warranty as to fitness of purpose or merchantability, subject to the laws of the state of (your state or province.)”
I’m not a lawyer, but I slept with one once.