I have to say that if you have a new mac, then you have really wasted a lot of time re-building your site in iWeb. Why on earth did you decide to do that when iWeb is so old and outdated?
There are many better things around that you could have used that are actually current and being updated and will work, unlike iWeb now and it os only going to get worse.
Why not look at trying EverWeb, which is a direct replacement for iWeb? You would not have all these problems.
For your current problem however, it could be FileZilla that is causing trouble. I used FileZilla once when I was using iWeb a long time ago now and I had problems with it, missing out files and not uploading, so I changed to Cyberduck and have used this to connect and upload and never had any further problems.
Try Cyberduck instead - download it for free and then delete the files that you uploaded with FileZilla and then re-upload them with Cyberduck and see if that makes a difference. Transmit is another good one to use, but you need to pay for that.
In the meantime, do consider moving to EverWeb, because I really think you have wasted your time re-building your website in iWeb on a new mac when iWeb is so old now, no longer sold by Apple and unsupported.