I had an issue recently where a client was editing Word documents on a server and when they went to save them, they would save but they were hidden.
You could drop into the Finder and unhide them by running
chflags nohidden /Volumes/Server/path/to/document.docx in the Terminal
This is obviously less than ideal.
As it turns out, the solution was to connect to the server using Go > Connect to Server (or ⌘ K) in the Finder, instead of clicking on a saved shortcut to the server that was sitting in the Dock.
For some unknown reason, when you connect to the SMB share via an icon in the Dock, or via a shortcut, it applies the quarantine flag to the server mount. If you connect to it via ⌘ K, it doesn’t seem to do that. Also, for unknown reasons, Microsoft Word has a problem with this, whereas other Office apps (e.g. Excel) seem to be OK.