I'm using an SFTP monitor to monitor a directory. When I created the monitor, it found all the files and they all showed up in the File Transfers pane, with status "Monitoring". They also showed up in the Log Files & Filters pane.

For the most part, this works fine, but sometimes, files just disappear from either or both panes, even though they still exist on the server. Sometimes they come back after a while and other times, I have to close and reopen the workspace to get them back. For example, I currently have a file that exists in the directory. It disappeared from both panes, but now, a few minutes later, it's showing up in the File Transfers pane, but it's still missing from the Log Files & Filters Pane.

It's the same issue as before. The transfer log is difficult to work with because it only works the first time I open it. If I open the transfer log, then switch to a different log file, I'm no longer able to view the transfer log after that. Therefore, if a file disappears I have no way of viewing the transfer log to see if anything happened. By default, SFTP transfers aren't logged on the server. I guess I could enable logging, but I'm not sure if this would provide any useful information.

Try viewing the client transfer log from the File Transfers view.  Logs are written to disk, so they shouldn't disappear.