Question about using FileZilla

I posted earlier a question ("Couldn't sign in to your FTP server. Timeout was reached") about my problem publishing updates to my site in which the transfer was always terminated because timeout was reached. (Previously I never had this problem). Several people gave good suggestions but unfortunately none of it worked. My server is hosted by InMotion and they suggested I use FileZilla.

I have exported the site to a desktop directory on my Mac and apparently I just need to drag these files to the public_html folder on the server. However, when I look in FileZilla and compare the contents of the folder on my local site (the Mac) containing the files from the export with the contents of the public_html directly on the remote site, there are many files on the remote site that are missing in the export (see screenshot from the FileZilla app). Should I nevertheless just move these few exported files to the public_html directory on the remote site?