Just to confirm, are you sure that your files aren’t deleted for any of the reasons listed here?
If not, then can you please describe a little bit more about what exactly you’re doing so we can try to reproduce it? Are you uploading a specific zip file we can access, or can you at least tell us the size of it (the total MB of the zip and the number of files in them)? And where exactly are you trying to upload it (which account and directory)?