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:
Behind Altar in the church.
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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?
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!
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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.
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.
For the most part they fixed that
The start of the monestary quests you no longer lose the items in your quest section. Also after I completed the monestary quest I got my stuff back at the very end. I only had 4 clothing items cause I was warned that you had to empty your inventory before u enter and u lose stuff etc… I got all my clothing back all 4 items. And they never took out the quest related items or items under quest in inventory.
