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.
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