EPUB3 has the potential to be a solid format for preservation when creators (1) abide by the official standard; (2) keep to core media types; (3) avoid encryption; and (4) encapsulate all required resources within the EPUB file. Including large files, remote resources, or interactive features, however, can make the EPUB large and therefore impractical for general distribution. Where the publishing platform has mechanisms for generating EPUBs, implementing a workflow for a preservation-specific EPUB3 that can be created alongside the public-facing ebook would be a boon to preservation services.
When preserving a website rather than an EPUB, this guideline may be relevant:
58. For a custom web application, consider encapsulation early