The new Elephant version comes with some new features that will make life easier for SEO. The most relevant are:
Previous to Elephant URL-as-parameter, BrightSide Publication URLs were generated using the publication ID. Something like ?item=n. This has been override by easy-to-read URLs. Something like /elephants-new-features-for-seo, which happens to be the URL for this one you're now reading.
Currently, the URLs are auto-generated when the publication is saved. And wont change in future savings. The new system is backward compatible with the previous one.
The URL-as-parameter generates when publication entities have their own context defined. See Sitemap.
The links affected (but not exclusively) are:
Elephant generates a sitemap from all its contexts. Also, requires BrightSide modules to provide relevant URLs. See Sitemap for more information.