1/4" is about the max you can use with thinset, but yes, it should work. I'd burn it into the surface to get good adhesion (it's always a good idea to take a sponge and wet Hardi before applying thinset - it sucks moisture quickly) then use a long straightedge to screed it flat. Thinset sticks to thinset fine, and will stick to the cbu, especially well, if you clean the dust off and add a little moisture prior to application of the thinset. For this app, not as important as when setting tile. When setting the tile, you need some time to get them installed. Here, you don't really care if it is still sticky since you are using it as a filler.