When something is considered retroactive, you are to treat it as if it was always the case, even though it wasn't.
For instance, if you gain enough of a permanent increase to Intelligence to raise your modifier from +4 to +5, you gain the skill points (and other benefits of Intelligence) for each previous level at which you didn't have that bonus, as well as for the current level, and at every level you gain after, per a response on a forum thread.
This has the effect of simplifying the working out of hit points, skill points, and other aspects of high-level character generation, such as languages known and spells scribed.