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Believe it or not, but I think this resulted in my strange behaviour earlier as well. I just came back to found out at still using version 4 of the moss plugin. After I updated to 4.01 and updated DynDOLOD I don't have anymore issues like the vanishing windmill and also the honning brew meadery buildings are either LOD or full model, no more overlapping - I used the exact same method as before where the problems were, nothing. Everything is normal now.
Also I did the regen with alpha 102 if it