How to deal with missing/loose knots

I live in Southern California and have a 20-year old poorly maintained redwood deck I cannot afford to replace. Half of the deck is in full sun and the boards have splits and missing/loose knots. I have flipped the boards which helped with the amount of splits, but the knots are still a problem. I plan to replace the worst boards, wait several months for them to weather, then clean/brighten and apply AC semi-solid Stain.  I am guessing that any type of wood filler applied to the knots will not accept the stain properly? Anything else I can do besides replacing the boards? Also, if I need to sand will those areas stand out?

thanks!