If we are, in fact, living in the Matrix, then science has already characterized the rules of the simulation rather well. Barring further interference by the sysadmin/God/whatever, it should continue to operate by mechanistic, semipredictable rules. Science has little to say about one-time interventions from outside observable reality, whether you call them "Matrix hacks", "miracles", or what you will. Regarding such matters, the null hypothesis has yet to be convincingly falsified, but absence of proof is not proof of absence.