This happens when you open the system, save it and exit without loading CSGs. The metal spot placement will remain the same but all customly placed CSGs will be removed. It's so frustrating when it happens. T.T Now i'll export a backup as soon as i feel the map is finished
The map editor is so broken and it has always been broken. It is a very big pain to work with. Yes you can do a lot but it is very hard and annoying.
Knowing that it exists is about the extent of my knowledge - https://forums.uberent.com/threads/wip-map-system-editor-fixes.68511/