Obviously, the generated UV map is just the one UV map on top of the other UV map and of course the result is overlapping lightmap error and something like this:
Open up your merged mesh in static mesh viewer, and check these params:
Source lightmap index indicates UV channel, islands from which will be used to generate lightmap UV.
Destination lightmap index is UV channel, where new lightmap will be placed.
Try both to 1 and 1
Also, the issue you are having, could occur due to unclean mesh, so make sure it has no unwelded vertices or something similar to that.
Thanks, you’re right! Changing source and destination index to 1 create a good UV map. But why I have to do this for every merged mesh? Source meshes were using 0 has source and 1 has destination. The merged mesh was generated with UVchannel 1 has target lightmap.