It looks like after the merge, model quality of default LOD degenerates, I’ve been messing with the settings but can not get a merged mesh that matches with the original one.
I don’t know whether you have already solved or abandon this problem. Just in case others encountered a similar issue, I share my work around here. Before merging, I just saved another version of original model with Nanite disabled. Then the system would recognize its Nanite triangles as LOD0 triangles. If I used that for merging a new mesh (with Nanite enabled), all the triangles so that the quality would be preserved. Hope this information helps.