It is probable that the file “.backup_time” is being generated by a backup system that is running in the server where your website is being hosted? If this is the case then you should not delete that file because (according to its name) it seems to be tracking the time of the last generated backup, if you delete that file it will probably confuse the backup system.
What you can do is to select that file and mark it as fixed, that way the plugin will ignore it in future scans considering that it does not seems to be malicious. Note that the plugin will keep monitoring the modifications of these files even when you have marked them as fixed.
Regarding the issue with the FTP client, I do not know what you software you are using so I can not give you a definitive solution to fix that, but I can explain you one possible reason. Do you notice the single dot at the beginning of the file? That dot forces the file system (in most Unix operating systems) to hide it in the directory listing. It is probable that your FTP client has an option to display hidden files.
Another reason could be that the file has no read permissions for the FTP account that you are using. If you consider that the FTP protocol is based in the execution of basic plain text commands you could suspect that these commands may fail from time to time. For instance, it would be possible to execute a command like “LIST”, “MLSD”, or “NLST” to list the content of a directory and only get the files that are readable by the FTP account used in the connection.
Let me know if you need more information.
