I use Photomatix batch merging process for my real estate pics (RAW). I like the results i get with LR but don't know how to do batch processing ???
As far as i saw it i can only do 1 or 2 sets and that doing them separately too!
There is no batch option as far as I am aware. You have to select the HDR sets of images series-by-series and invoke the HDR merge option on each set individually.
Many people have asked for batch merging. Add your opinion and vote to this topic in the official Adobe feedback forum: Lightroom: Ability to batch process HDR brackets. That topic also explains how to start a merge immediately without being asked any questions.