I have several different situations. Some places, like where the irrigation system doesn't hit the concrete, the wood is fine. Other places the wood is completely rotted away. Sounds like the consensus is to remove the rotten wood, fill with sand leaving about a quarter of an inch for the Sikaflex. Thanks for the tip on not touching it.
I really think sand is the wrong material. Please read Allen's link, which explains why better than I did.
http://blog.poolcenter.com/article.aspx?articleid=6289
Or go take another look at the Amazon page you linked. In addition to the Slab Gasket product, it's filled with alternatives, each of a pliable material. By definition of purpose, an expansion joint needs to expand and contract. Sand does neither.
If any of the wood you're replacing is in an expansion joint, or if you don't know for sure if they are expansion joints or not, don't use sand. If they are not expansion joints, then I suppose sand is fine, though backer rod is very easy to use. Not to mention a whole lot lighter to get from store to car to yard to joint!
The following is conjecture, but something I'm going to be trying. If you're dealing with expansion joints, they move around. And can move a lot. They'll be larger at night (the surrounding material got colder, and contracted), and they'll be smallest at the end of the hottest part of the day. They'll be larger in the winter than in the summer. The amount of the difference could be as much as 1/4". Maybe more. If you apply the caulk while everything is hottest, then you run the risk of the caulk pulling away, or splitting down the middle, when everything gets cold. Conversely, if you apply it in the dead of winter, then it'll bulge a bit come summer (which is better than splitting). That's what some of mine looks like: pulled away and/or split. So I'm going to try to caulk when I estimate my deck is at or below its median temperature: probably late morning, in the late fall, maybe on a cloudy day (no sun). I'll know in a year or two if this idea has any merit, if my caulk holds up better than my first attempt did, which I applied mid day in summer. It only lasted a few years (and maybe in part because I didn't use Sika, but a cheaper brand instead, which I won't use again).