I'd created several subfolders on that drive and I'd successfully copied thousands of files over. I saw there was a 16GB file in the root of the drive that I wanted to move to a folder (/media/16TB/D) so I right-clicked on it, selected "Move To" and typed in the target folder. It seemed to be taking a long time, considering that it just needed to move the file from one folder on the server to another, and then WinSCP started showing errors about other files and quotas, even though I haven't got the quota tools installed on the server and haven't set any quotas. When I looked at the folder after that all the files were gone, apart from the one that I was trying to move, and even that hadn't been created properly.
Unfortunately I don't have a log from WinSCP, because the default settings have the logging disabled and I didn't know that until after I had this problem and read the instructions here about posting a bug report. I've asked in the Debian forum if there are likely to be any logs on the server showing what happened. I guess I can try to reproduce the error, but I can't create the exact same conditions as the files that were in the folder have been deleted. I tried recovering them with testdisk on the server to another drive, but that just recovered the subfolders and none of the files.
I took this screenshot (also attached), showing the "Space Available" details for the drive, which shows that only around 2TB is used and 12TB is free, but even if the drive had been full that wouldn't explain why the existing files got deleted rather than the command to move the 16GB file failing. https://ibb.co/zGyw53w
WinSCP version: 6.1.2 portable
Windows version: 10 20H2
Transfer protocol: SFTP