Troubleshooting, summarized:
If, for some reason, iCloud Drive seems not to be syncing correctly, all you have to do is log in and out of iCloud, run some commands in the Terminal, re-download or re-upload many gigabytes of files, and then simply do it again whenever you want it to actually sync.
It's basically like having a hard drive. Only the hard drive is a Fiat someone drove into a river a couple times.