The memory issue and the kuka smartpad freezing is a known issue and I have been facing it every now and then.
You can validate if this related to the same issue I am talking about, by doing a cold restart of the system. The system starts behaving normal until one point where the hmi freezes out and handling smartpad would be impossible.
Regarding the movement of files to D folder, what kuka claimed, everything under the R1 folder would be loaded to the ram and would stay in the virtual memory. The more garbage files exists, the slower the pc is going to behave.
One more situation where I have seen this happening is writing too many temporary messages. Kuka advised to store messages to variables and write and erase from the variable before loading the next one. loop messages remains in virtual memory blocking spaces and when infinite loop messages are written, the system starts behaving strange. I assume same applies to submit.
Talk to kuka, they usually have a ready made solution in the form of software updates / patches for this as this is not a new problem and it exists since kss 8.3 and i am seeing it also sometimes at kss 8.7.