Copying files not found on iCloud backed up folder

I have a project folder that contains various .py (python scripts) files. When I copy said folder from a non iCloud folder and paste it (or move) to either Desktop/Documents, there are 2 out of the 8 script files missing. I can copy them manually and it works but not when I copy the root project folder entirely. I accidentally did moved various project folders to my iCloud Documents folder and now some projects don't work because iCloud seems to be randomly deleting files.

I want to know why this is happening, if iCloud can delete random files as it likes, I will stop using it.