as for prophecies that we now prove is true retrospectively:
1. That is the only way to accurately and in a manner of science prove it. If it didn't happen yet, I can't prove to you that it is true. But if it did happen, and G-d had predicted it, I have "scientifically" sound proof.
2. There are other prophecies which have yet to come true. I can't prove that they will come true. That is belief. I believe they will come true, because to date, anything promised so far has happened. Therefore, if you want to debunk me when they come true and I say "aha, told you they'll come true" you can read them now so you know the prophecies were in place before the event occured and were clear prophecies, not embedded, encoded ones.
3. Just as with prophecies coming true, science ends up proving what we have been taught by G-d centuries ago. Therefore, where the two don't coincide I will stick to G-d's version, and wait until science catches up to the reality. An example of this would be the length of a lunar month, which had been the basis of the Jewish calendar for thousands of years - and which calculation has been proven true because NASA, with the new-fangled tech, has come up with the same exact figure. Hence, I have no problem where my religion and science don't jibe. I realize science is an "evolutionary" process and will someday catch up to our realities.