According to the wiki it says to repack bsa's back into bsas if they involve more than just textures/meshes
"If you did not include any of the BSAs from the Dawnguard, Hearthfire, or Dragonborn DLCs, which contain multiple resource types in addition to textures, you can ignore these final steps. Now it is time to package the rest of the directories, if any, containing optimized versions of any of the these DLC BSAs you created. Unlike the directions for the optimized versions of the STD and HRDLC BSAs which contain only textures, we suggest that these be repackaged into BSAs since they contain a wide variety of resource types, not just textures. The notice above tells how to do this. Put these new BSAs into the Data directory, where the original BSAs that you moved in the previous step were originally located, as the output path. Use the name of the original BSA as the file name. The optimized BSAs will then replace the original ones. For example, the file name for the optimized Dawnguard.bsa would be "Dawnguard.bsa". Alternatively, you can use the same approach as we recommended above for the other BSAs and archive the folders as loose files."