KeyShot 8.2.80
iMac (Retina 5k, 27-inch, late 2015)
MacOS 10.14.3
4 GHz Intel Core i7 CPU
AMD Radeon R9 M395X 4096 MB GPU
64 GB 1867 MHz DDR3 RAM
Regarding the CAD software, if I'm modeling the object myself, I have the object split into the parts I need before I ever import into KeyShot. When I model, I use Rhino 3D on Windows. But it's not too often that I'm doing the modeling. Typically, I work from models purchased or downloaded from other sources such as TurboSquid, so the original CAD software varies. It's with these models that I need to split parts using the Geometry Editor. From what I have noticed while working with Rhino, when objects in 3D models all have the same name (or more commonly, no name at all) and are exported as an OBJ, KeyShot will automatically combine all of those separate-but-similarly-named objects into a single part. This is the reason why I have to split objects so often in KeyShot.
I'm fairly certain now that the key action that causes this to happen is reorganizing the parts list in the scene window - specifically, moving the split objects out of the group in which they are automatically placed once the Apply button in the Geometry Editor is clicked. I've heard it before... reorganizing the parts list is not standard practice... I know. But I have over a decade of experience working with Photoshop for a living before learning 3D modeling and KeyShot, and much like layers in the layers palette of Photoshop, it is absolutely vital for my sanity to have objects in the parts list of KeyShot's Scene window organized the way I need them.
As for replicating the issue: Depending on how the model was designed/built, I will either Split Object Surfaces or Split Separate Objects. Once I split the objects and click Apply, everything appears as it should. I can even apply materials to the objects that I just split, and nothing seems out of the ordinary. But if I reorganize those objects in my parts list (which I am going to do, regardless of what anyone tells me), then save the KeyShot file, close it, and reopen it, the parts that I did not split still remain, but the parts that I did split are gone, nowhere to be found.
My uneducated guess is that the group that KeyShot automatically places split parts into has an identifier associated with it. Once the now-split parts are moved out of that group, the split parts lose that identifier and KeyShot forgets they exist.
I uploaded 3 different files to WeTransfer. The first is the unedited object. The second is the object split into separate parts, but not moved out of the group KeyShot placed them in. The third is basically an empty file because I split the object, reorganized them in the parts list and saved the file - now they're gone.
Note: I uploaded .bip files instead of .ksp files, as I could not replicate the issue when saving as KSP. It doesn't seem that anything included in .ksp files but not included in .bip files has any effect on the outcome anyhow.