I've had the issue in the past with my FTP becoming "disattached" from my Family Site. For instance, If I had 750 people in my tree and I synced it to the website, a couple weeks later, FTP would say I have not set up a website and when i would try to sync, I would get an error because its trying to upload all 750 people into the remaining 250 slots. So I would have to go in and delete the family tree and then reupload.
But with the new design, I cannot find the same functionality to delete family trees that used to be there.
Also, FTP really needs to come up with a better way of selecting people to update. If I don't want to pay for one of the premium sites, I need a better way of selecting which 1,000 people I want on the site. The only way now is individually. So I have to go in and select 1,000 individuals. Not going to happen.