Should I change settings between runs?

Settings changes take effect on the next run and never retroactively re-judge completed changes. So changing them is safe — but changing them often is counterproductive.

If you adjust the target every week, you can never tell whether a result came from the changes or from the goalposts moving. Give a setting several runs before deciding it is wrong.

Every settings version is recorded, and each run freezes the version it used, so you can always see what rules produced a given decision.