You can be absolutely sure that the file was not deleted by the system. So it is not a DriveHQ issue. You can verify it by uploading a file with any regular FTP client program such as FileZilla. If you upload a file via FileZilla, it will not be deleted automatically, which proves the FTP server does not delete your files.
So you need to check if your program automatically deleted it.Try a few times and see if you can duplicate the problem.
Please note the FTP/SFTP feature is a business feature and requires a business subscription. You can try it with a free or personal service plan, but it will stop working after some time. (It has nothing to do with file deletion - it will only block the FTP/SFTP connection after some time). You can also sign up for a free business trial.