I think I solved this...
Instead of the Windows application, I used the browser-based version of iDrive.
https://www.idrive.com/idriveent/remote/devices
(You will need to login and provide your encryption key)
Navigate to the problem drive, then to the problem "File Missing" file(s).
Hover over the file, and you will see and 'x'.
Click the 'x' to remove the file.