By default, 3D-FTP uses file list caching on remote servers to speed up its file operations. The caching means that the file listing is read only once from the server and then saved to the local hard disk; then on subsequent requests, the file listing is read from the local hard disk. By default, the local cached file listing is reread (=refreshed) from the server after it is over 1 hour old (see Site Editor to change this setting).
This caching causes you to see file listings that might not contain all the files and folders that are on the remote server, or to see file sizes and dates that are not up-to-date. To manually refresh the file listing (=command 3D-FTP to reread file listing from server), hit the F5 hot key or select the Refresh command from the file list right-click menu (right click on top of the remote file list).
Related
Cache settings in General Settings