Bondo can work well, but you have to 'force' it into the groove. You're right, it won't flow fluidly into it. I just take a spatula or paint spreader and push it down, then re-pour on top. It should be good to go then.
Alternatively, I've had some successes with Wood Filler in the slot and re-cutting. You just gotta pack the filler into the crevices as well as you can, and really make sure it's dried/cured before you re-slot it.