Ok, I lied! I'm not done with this game.
It says a lot about PoE (and how much I want to play it) that I'm stubborn enough to work on this stuff for hours.
DISCLAIMER: I don't know if this fixes everything. I don't know if this breaks anything further down the line. So far it works for me. Here is what you need to do.
1. Install IEMod
http://rien-ici.com/iemod/
2. Load any game back up where you missed out on Maerwald's soul.
3. Input the following console commands (you can copy-paste them) depending on the outcome you want:
a) If you wanted to absorb his soul, type in the following commands: SetGlobalValue b_watcher_chamber 1 [i don't know how to open the chamber yet! It should be possible but I do not yet know how! Use this one at your own risk!] b) If you wanted to free his soul, type in the following commands: SetGlobalValue b_watcher_prestige 1 AdjustPrestige 1 c) If you wanted to bind his soul to the keep, type in the following commands SetGlobalValue b_watcher_security 1 AdjustSecurity 1 Once you've done one of the above, also type in the following two commands: AddAbility player speaker_to_the_restless StartQuest data/quests/critical_path/act_2/cp_qst_ff_ruins.quest
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Once done, you should be good to go. This will begin the next quest properly, give you the Watcher's ability, and give you the boon for releasing/binding his soul. I do NOT yet know how to open the chamber at the bottom of the Endless Maze as I have not gotten that far yet (nor will I for some time), so if you want the treasure pile, use it at your own risk. Most likely it should be possible to unlock the chamber or acquire knowledge of it somehow once you're on the bottom floor, but I cannot be sure of this yet.
For now, I'm going to keep playing until the next thing breaks.