Ok, I think I have found some very relevant information through my research. The same exact thing happens when level is extracted to another module. I tried several times copying a basic level from a module to another module and it always ended in "Source Control". I then found through digging with the lstools that every object in a module has a map key. This seems like something set in to prevent copying other peoples work. What I then think happens when the auto optimization occurs is that it makes a new terrain with the newly optimized version of the terrain and replaces the original, but it doesn't have the proper mapkey. To avoid this optimisation bug, one could perhaps have all the map keys of their different terrain objects in a seperate text file and then replace the keys in the terrain files when the optimisation occurs? Could be worth a try.
