You know what happens when you flush too early?
Not all the poop gets washed away... And in the case of rewrites, that means some poop might not have come out yet.

Also, let's just flush every time the plugin gets upgraded. Improves the chance of our rewrites actually working.
Add a comment in the code.
Merge pull request #1788 from Yoast/flush-properly

You know what happens when you flush too early?