I made a choice hundreds of hours ago which prevented me from getting the best ending (aka the "tempered" Abydon ending). After a crazy amount of searching, I figured out how to get the ending I wanted without have to re-do all of that.
1) Open your game folder, then open the Pillars of Eternity\PillarsOfEternity_Data\data\conversations\px2_04_eyeless_stronghold folder.
2) Using Notepad or a similar program (I prefer Notepad++), open the following file: "px2_04_cv_abydon_finale.conversation"
3) Locate the following segment (for me this was around line 7676):
Change the "Not" section from "false" to "true" (I also changed "And" to "Or", but I don't think that's strictly necessary)
<ExpressionComponent xsi:type="ConditionalCall"> <Data> <FullName>Boolean IsGlobalValue(String, Operator, Int32)</FullName> <Parameters> <string>n_abydon_arguments_won</string> <string>EqualTo</string> <string>3</string> </Parameters> </Data> <Not>true</Not> <Operator>Or</Operator> </ExpressionComponent>
4) Save the file. It's good bookkeeping to keep a backup of the original file too.
5) Load to any point before you tell the Eyeless whether they should reconstruct Abydon or not.
6) Choose a few conversation options and you'll see the new choice "Then return to Abydon with perspective as well as memory". Choose this option to get the best ending. This bypasses all other requirements by the way: You can leave the Readcerans alive, you can permit animancy, do whatever you want. As long as you choose that conversation option, you'll get the good ending.
Hopefully this will help others. Good luck!