Several of the issues of Libram Novus were released during the Open Beta process, and therefore do make references back to it. At the time that they were written, this made sense and was not an issue.
For example, when LN#2 was first released, each magic using class was originally listed separately. We changed that, and so I went back and added that Class Addendum to the PDF, to explain why there are classes listed out separately, when all of the magic using Classes are grouped under 2 more generic classes in the rules.
Perhaps I need to update it again, so that it simply references "during the beta process, things changed" and then note how to use those classes in conjunction with current rules.
Something similar happened in Libram Novus #3, where a change in the core rules was being made and that explained one of the reasons why it was included.
However, it has been over a year since the end of the Open Beta and the release of the final version of the rules
Therefore, you are quite likely right that those references remaining in thereare quite possibly confusing, especially for folks who were not involved in the Open Beta (something that honestly would not have occurred to me), so I will go back and take a closer look and see if it is possible to reword things a little better (besides, I think there are a couple of other tiny fixes/corrections that need to be made, to Libram Novus #3). Once I update the files, I will re-upload them to RPGNow, and send a notice from the store that the updates have been made (and you will be able to go back and re-download them at your leisure.
And please, if you find any other possible errors/mistakes, bring them to my attention, so that I can double check them and fix them if needed.