I don't think they did. The way I understood it is this:
If you go via "Sources" and choose the book that you own, the content in that book will be the version as it was originally published in that book, modified by any errata that was released for that book.
But if you access that content via their general listings, or via the Character Builder, it will be the most up-to-date version of that content, regardless of book.
So, for instance, let's say that Book A contains a playable Modron race, and a month after it was released, an errata was published which corrected a glaring error in the Modron's design. Book B, which was published a year later, contains a tweaked version of the Modron race, which is intended to replace the one published in Book A rather than serving as a variant.
If you own Book A on D&D Beyond, you'll be able to go into Sources > Book A and see the version of the Book A Modron as modified by Book A's errata. You will not have access to the pre-errata version.
Whether or not you own Book B, if you go into Game Rules > Races or if you open the Character Builder, the version of the Modron you'll find there is the Book B Modron.
The caveat here is that the Wayfinder's Guide to Eberron was specifically billed as being a living document that could be updated later. If the Wayfinder's Guide is updated to use the same version of content as the new Eberron book, that will be the only version available.