All changes made to point modifiers will be applied retroactively to all fantasy stats previously earned. Scoring will update the morning following the change.
So, if you are in a Custom League and the commissioner changes the value of a save from one (1) point to two (2), all teams will find their score in the saves category doubled the following morning.
It is not possible to make a change to your point modifiers and have that change apply only to future games.
At the end of the season, each team's fantasy point total in each category will be equal to the raw total they accumulated in that category multiplied by the final point modifier.