Files are missing message when using webdav

Welcome to the forum @Craft

Perhaps you can start by trying this not-yet-answered question from another invisible-Nextcloud issue:

Assuming these 3 files are small discardable test data, you could also delete them, then test the folder.

Duplicati.CommandLine.BackendTester.exe can take the URL obtained from Export As Command-line.

If you prefer to test remote operations manually, you can try Duplicati.CommandLine.BackendTool.exe.