The underlying problem of this story has two parts:

1. When modifying the rules that are used to evaluate which site should be served
2. actual link generation in ckEditor (possibly in more use-cases) might generate links that cannot be served anymore.

To put it differently: Site evaluation rules are not taken into account for link generation

(One of) The "problematic" rules is uri-starts-with-sitename which will resolve a site when the URI is prefixed with the actual sitename. Due to SEO optimization, it might make sense to move this rule down in the chain (on a side note: content should actually only be accessible through one URI only; this rule enables accessing content of different sites over different domains).

This becomes an issue when adding links in ckEditor which are actually prefixed with this particual site-prefix, now resulting in an invalid link (the rule to "detect" this link was moved).

breun has supplied thorough descriptions, analysis and steps to reproduce in:
SUPPORT-4685: Link creation the rich text editor
SUPPORT-4535: Cross site access

Notes

• uri-starts-with-sitename rules is mainly there to enable serving all sites when working in an admin instance (where access might indeed happen through one domain).
  • maybe it makes sense to only use this rule in the admin instance
  • and only generate link with this particual prefix on an admin instance too

Also an point to think about is:
In the context of link creation to other workspaces used by apps.
Linking to such items in combination that these workspaces are mapped in "URI2RepositoryMapping" and specifically added to a site definition's mapping.