FTP and statistics

I asked this question before but didn't get a clear answer. I just want to ask about this sentence I remember I read in an article but really forgot the source:
+FTP upload puts the entire site into a separate folder, and this may affect statistics+
Does it mean here that RANKING is the issue? How is that then?
Thanks.

When you use iWeb's FTP only the changed pages are uploaded.
Search engines are capable of seing the changes.
I make a lot of changes to my site. My current ranking is somewhere between 3.500.000 to 4.000.000.
I hardly notice a change.

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