We had a similar issue (ie, same bug but no data layers). In our case the source of the problem was that a StaticMesh asset was being referenced by a foliage actor, but the StaticMesh had been moved in the directory and the foliage instances in the map were confused. The easiest fix (which I was able to replicate a couple times) was to select all the foliage Instances in the outliner and select Save Selected Actors. That fixed it in our particular case!
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