I assume you're talking about the merged rows feature of CBC?
Let me clarify the way that merged rows works and maybe that will answer your questions. The merged rows feature in CBC is strictly a display feature. In other words, The "merging" of the attributes happens after the design has already been generated. So in the designer, as well as the analysis tools, will still treat all of your attributes as individual attributes even though the respondent saw them as if they were all combined into one.
So if you have attributes A, B, and C with all of their individual levels, perhaps they all represent different levels of different features of a product, you can merge those levels together and label the new merged row as "Features". When you generate your design, the designer will still say that concept one should have attribute A level 1, attribute B level 3, and attribute C level 7. Then when the HTML is generated, there's code that sees the rule you have in place to merge Attributes A, B, and C so what the respondent sees is an "attribute" called Features that list A-1, B-3, and C-7 in that product. Then when you go to HB and the simulator, those tools don't know how the respondent saw those levels (as a merged row or as an individual row), they just know what the design was for that task and the concepts that were and were not chosen. So Merging rows is strictly a display feature for the respondent facing part of CBC.