Intellect distinguishes between the possible and the impossible; reason distinguishes between the sensible and the senseless. Even the possible can be senseless.
If God has made the world a perfect mechanism, He has at least conceded so much to our imperfect intellect that in order to predict little parts of it, we need not solve innumerable differential equations, but can use dice with fair success.
And the continuity of our science has not been affected by all these turbulent happenings, as the older theories have always been included as limiting cases in the new ones.