I can confirm that you cannot kill some NPC. Example the custodians in Sasau. I was angry with him for putting in jail for answering him “incorrectly” (as his point of view anyway…) so I went to kill him and whatever if I break any other quest. But as it turn out, you cannot even swing your sword on him ! I was even more angry, so I killed a bunch of people that passed by… haha Then I reloaded and searched my inner peace.
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Borked up reputation like in this case has a cure - you don’t have to revert to an ancient savegame nor start a new game.
Hit an innocent civillian, surrender to guards (G) and go to prison. All reputations will reset and the monk won’t run away from you any more. Or in another borked instance, the executioner won’t attack you on sight. Etc.
Note that this imprisonment will last 7-10 days. I have no idea if 1 day of jailtime when caught just for pickpocketing in public also resets reputations with NPCs.
Additionally, I have no idea what stash is talked about in the first post here. A quest item that you have in inventory, you can’t move into any stash.
Yeah can you tell me exactly what quest item not to pick up because I’m about to head to Sasua, not long started game really, but I like to explore everywhere before starting main quests but I hate it when quests for an break because of that. Than it shouldn’t be open world if shit like that happens
Feel free to grab Necronomicon in the Monastery before you get the quest. I did it before I knew what’s it for, solved the quest normally later when I got it.
Another example is Adam’s Family Cross (loot from a chest in certain cellar - won’t spoil). Didn’t know what’s it for, much later I successfully solved a quest where it’s required.
For all I know there is no quest item you shouldn’t take before you get the quest.
However, this does not apply to nonquest items!
There is at least one bugged script - note that in this case there is NO quest item. Not a single item is marked as quest item:
http://steamcommunity.com/app/379430/discussions/0/1700542332339188140/?ctp=158#c2860219962090595583
Lost in Translation quest is severely bugged. At least in my game:
- Cuman is invisible thus the only option that won’t stop the quest from progress is to accept to help Miller. It’s not possible to threaten Miller and then talk to “a ghost”.
- If the player finds the treasure before talking to Miller, the quest will get stuck on “talk to Miller” step, it’ll never progress with “give half the treasure” step.
- If I lie to Miller succesfully the quest won’t close, it will just remain stuck in the journal till doomsday.
Not being able to finish a quest because you already have the quest item in your inventory before you start the quest isn’t realistic at all…
“Hey get me this item. Oh sorry I can’t I already stole it but it accident melted into my inventory permanently”
Yeah I got the books during a monastery quest and now i don’t even know what am I supposed to do with them. Which NPC gave you the quest of retriving those books?
I did same thing. I just bought lockpick (spoiler or you can also find one - I can tell you where If you want) and you can get OUT same way you probably got in before - and in that room where you were, ehm, resting at beginning of this quest, you find ALL quest items - and they wont go away from your inventory no matter what happens later.
Hope this helps. I had same panic attack as you 
but I solved it this way.
Those items just can’t disappear I guess. So that’s great… I have finished main story today, but I took my time. Total of 109 hours played… and there will be more
Edit: another little spoiler Also one little hint where to get “money” for buying lockpick… potions
When you go into the monastry as undercover Novice during ‘A Needle in a Haystack’ , you have to leave all your belongings and get changed to Novice uniform. So all of your items, including quest items will me removed from your inventory will go into a trunk which is inside a corner room outside of the main monastery building.
I may have cheated for the monastery quest by just going into the would-be-monk’s room, and stealing the piece of paper while they slept for an infinite amount of time.
The issue here is that, during ‘A Needle in a Haystack’ your items, including the quest items will be removed from you and placed outside of the monastery. Since you cannot get out from monastery until you complete the main quest, you won’t have the quest item in your possession to complete the quest.
.Just to let you know, this book stealing quest is side quest so i don’t think it affects the main quest.
I forgot the name but there is a monk, who talks about helping old Abbot to recovering from his illness or something. You can get the quest from him.
I’m not at that point of the game yet.
When I do… I’ll post if there is such problem. So far there wasn’t.
I don’t know if you have already found a solution because I am too lazy to read all the comments!
But there is a way to get your quest items while you are in the monestary.
Solution includes sneaking out of the monestary and search near the big entry gate 
I won’t have any problems probably as my lockpicking is level 18 and I’ve finished the Questions and Answers main quest currently so can’t be 100% sure.
Previously I grabbed all torn pages in monastery I found which are, if I understood correctly, quest items in an upcoming main quest. Logically since I managed to break into that area (hard locks on the church and inner chambers) anyone who did the same thing before the main quest should also be able to break out.
So in a way he’s right - the quest “steals” quest items from you which seems as an oversight. But then again, if you broke inside previously and took quest items already, you should be able to break outside the same way.
Again, YOU CAN get out of monastery. I wrote how in first post in this thread. I was in same situation. I found a way to get all those items. It’s really not that difficult.
You did wrote, yes.
You don’t have to buy a lockpick if you find one, and that one is:
Spoiler
Behind Altar in the church.
…
There is a second option if you’re roleplaying non-thieving character, the same monk who can sell you lockpicks can also sell you monastery key for $200. Now where to find such huge sum?
Spoiler
Open the door in the sleeping chamber which will lead you to a sort of balcony. You’ll spot a trunk, who cares about it, because in front of the trunk is a lose stone - under it you’ll find a ceremonial dagger, $200 and, why noone told me this before I stole Necronomicon I for the sidequest a week ago, you’ll find Necronomicon II!
…
Thus I say again, feel free to get every questitem before you receive a quest. Nothing bad will happen and nothing will get bugged. In case you feel stuck, a little exploration will do the trick.
What about if you have never opened up the forbidden cabinet before and the two books are not even there? I thought maybe they could be invisible and I just had to get the correct position on it but there are absolutely no books on the left hand side of the second shelf.
I’ve hardly found them also, examined that cabinet 3 times. Try to search a bug description if no luck examine the shelfs better.
I think these elements of consequences for stuff you did earlier in your play through is really cool. It’s causing a lot of controversy but this game is closer to being true to life, bugs and all. So many times in life I might do something and everyone else will have no idea how to respond. If I choke a guy out and then beat up his friend before he talks to the police, it’s perfectly natural for the two of them to want nothing more to do with me. This game has more reason than say Skyrim to act that way. In Skyrim, the Dragonborn is literally the only person in the entire world that can save the world. So some of his actions might not be taken as seriously because they kind of need him to not die. Henry is of zero consequence to the greater picture. If he fucks up his reputation, Radzig and the other nobles can just find someone else.
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There is a lockpick laying around (corridor entrance). Also keys (kitchen). Take one of those, unlock a door to go outside and get your stuff back.