Hi,
Nope, there should not be any problem. The only time where the warranty is void is if:
1) You open your calculator case (although I wonder how they prove it)
2) You damage your calculator with a third-party software. This should not happen unless you really do something bad that you shouldn't. Otherwise, most software failures can be resolved by sending a new copy of the OS anyway.
Point #2 is why the current Beta of Ndless 2.0 is not distributed in compiled executable format.