Waveboxes tend to stir up detrius that previous means of flow couldn't do... potentially you could be getting detrius settling on the chalice causing it to recede - just watch for that.
Generally speaking a WB will not harm any coral assuming the coral isn't being blasted like a tree in a hurricane (this goes for any type of flow, WB or not), and on the flip-side assuming the coral is receiving appropriate amounts of flow.