Hi there!
This is a known bug with the file tree in the Agent Window (Glass layout). When files are created or modified (especially over SSH remote connections), the file tree doesn’t always refresh to reflect the changes.
Our team is actively working on a fix. In the meantime, you can work around this by using Developer: Reload Window (Cmd+Shift+P → type “Reload Window”) to force a refresh.
You may also find this related thread helpful, where another user reported the same issue: File tree in Agent Window does not refresh