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I've updated my entire site all at once several times over the years. I also continually update older pages and add new ones and/or change the overall layout and/or color scheme.
Problems might arise only if you ignore what is currently working for you - the current navigation structure, content, incoming and internal links, anchor text, <Hx> tags, etc. because all of these are part of the ranking algorithms in one way or another.
If you have changed the entire site layout and rewritten all the text you would want to analyze these changes, but hopefully you planned that carefully before you reworked the site :)
It's Google's job to find the most useful and well-designed sites. Its reputation is at stake on precisely this issue.
So, if you factor well-formed markup, standards compliancy and accessibility into an easily navigable interesting and useful site... then if Google doesn't rank you very highly at first it soon will, because _it will look bad_ if it doesn't!
I know that SEO involves a certain amount of looking at the positions of the search engines, but in general, I strongly believe that site designers should concentrate on designing excellent sites and let the search engines chase after them... rather than chasing after the search engines themselves.
When I'm designing pages I think about Google a little bit, but I think about well-formed markup and accessibility and intuitive navigation a great deal more.
When I'm designing pages I think about Google a little bit, but I think about well-formed markup and accessibility and intuitive navigation a great deal more.Agreed, the user comes first. But it would be shooting yourself in the foot to switch all your links to flash, or javascript, regardless of how intuitive the structure appears.