One of the biggest factors in the traffic you get from search engines is the inbound link profile to your site. When you make a significant change to your site, one question that the search engines need to consider is whether those links are still valid.
Would the person who linked to your site still link to it if they looked at it again now? If the answer is no, the search engine doesn't want to count that link.
Of course, the search engine can't determine the answer to that question, but they can choose to initially reduce the effective value of those inbound links for a period of time, until they see whether people start removing links to your site after you make a large change.
This filtering process helps protect them from spammers who look to buy domains with lots of link authority, and then change them into entirely different web sites (e.g., buying a domain that used to be for an educational institution and turning it into an auto insurance site). The people who linked to the educational institution certainly didn't mean to endorse an auto insurance site.
Let's look at a few cases where the search engine may consider a change large enough to reconsider how they treat your site.
Many website publishers make the decision to change their domain. For example, maybe they started out with a ".net" domain and they were able to obtain the ".com" variant of the same domain. Or perhaps they are simply rebranding their company.
Whatever the reason, a domain change in potentially seen as a huge change by the search engines, particularly if you do a site redesign, change the URL structure, change the content significantly, and change the WhoIs all at once.
Even if all you do is a simple domain change, the search engines have reason enough to contemplate the possibility that people who linked to the old domain would no longer choose to link to you. With a simple domain change and proper implementation of 301 redirects, your risk of a significant setback is relatively low. But the risk is still there.
2. URL Structure
It isn't uncommon for sites to go through complete redesigns, or to implement a new content management system (CMS) without making significant changes to the content at the same time. However, it takes time for the search engine to understand the new site structure to determine what is on the new version of the site.
All the intricate relationships between the pages of the site have been restructured, and this may take weeks or even months for the search engine to understand. In the meantime, they may feel a need to devalue your site somewhat. Implementing 301 redirects from the old pages to the new pages will help with this problem, but it doesn't eliminate it entirely.
Significant changes in content can also give a search engine a reason to ponder how it treats your web site. Even if the basic topic matter is unchanged, it can take some time for the search engine to make that determination.
When you make a change to the Whois record for a domain, even when no change is made to the domain itself, this can be an indicator of a change of the owner of the site.
To the search engines, much of the reason why one web site may link to another may be very much related to their trust in the owner. If the owner changes, is that trust still there? In many cases, the answer may be no.
Simply changing the e-mail address of the administrative contact isn't likely to be seen as such a signal, but changing the name or address of the registrant is likely to be interpreted as a change in owner.
Making such changes often goes without a hitch, particularly if you don't make other significant changes at the same time. Combining a major change to a web site and the registrant at the same time, however, starts to be quite a bit riskier.
Ultimately, the best way to change the registrant is to do it in isolation. Just wait a while before you make other significant changes to the site.
Changes in theme can take many forms. For example, if you have a site that is about auto insurance, and you then add a new large section on home insurance, it will certainly take a while for the home insurance section to receive the trust and authority conveyed by the inbound links. The value of the links to the auto insurance section of the site may also be devalued.
The type of change that would be seen as a theme change could even be a lot more subtle. For example, if you had a site that was purely a directory of links to auto insurance resources, with little text content on them, and you suddenly start putting lots content on those pages, this may also be seen as a significant change.
It gets back to core principle: Would the links that were given to a directory site still be given now that you've made a deep content site, even though it's on exactly the same topic?
Learn to consider the possibility of changes to your inbound link profile when you make changes to your site.
Will the change you're considering possibly impact those links? Even if the answer is no, you should also ponder whether the search engine will see the change as large enough that the search engine will question the ongoing value of those historical links.
Remember that the search engines use algorithms to make their determinations, and algorithms aren't as smart as humans are at figuring out what is a material change to a potential linker.