Okay, checked this. I don't have a merged.lsf file in the folder "LevelTemplates", as I'm building a standalone mod and don't overwrite anything from the main game this is the expected behavior I guess.
Went through the the instance group folders, they all contain a file named "group.lsf" and a bunch of "batch_##.lsf" files, so they basically look like yours. Also checked for naming collisions, all the folders have unique guids after the "group_" part.
So, just to add that, the instances show absolutely no issues in the editor, I can edit them perfectly and they show up as expected in the editor.
Last edited by DerCapac; 30/07/18 01:33 PM.