Chris has suggested this in the past:
1. Take the drive offline in disk management
2. Turn off all pinning in the CloudDrive UI
3. Clear the local cache, and wait until it's down to 0 bytes (literally empty)
4. Bring the cloud drive back online from disk management
You may need to repeat step #3 a couple of times to get this to work.
Specifically, this clears out the cache and forces the software to redownload the data from the cloud, including the file system data.
Setting the drive as offline ensures that drive data is not updated, and that any open files are forcibly closed (eg, without saving).
If that doesn't help, then CHKDSK or data recovery may be needed.