Some items with multiple versions have one version removed from the game but the museum still looks for that version.
Each of these items is a bit peculiar.
Honorblade of chorrol will autosort the LotD version of the sword if spawned in but will not check off the display in the checklist.
Ring of the wind seems like synthesis messed with it. There are 3 versions in the game data (from fishing, LotD, and tools of kagrenac). The museum wants 2 (one definitely from tools of kagrenac and one probably from LotD). Despite this the tools of kagrenac version does not have a TCC icon nor does it auto sort. *note I have yet to play ToK so I am assuming that the ToK version of the ring is what you obtain from the questline.
Ring of vipereye and ebony blade- both will take the removed item and place it on display if auto sorted. This will correctly check the item off in the checklist. Trying to remove both ebony blades from the display caused an issue where the museum could not find the item and opened up the entire museum inventory prompting me to remove it manually.
*Note There are 3 duplicate items that work correctly - keening, sunder, and wraithguard (one verison removed from LotD and another added by Tools of Kagrenac). When either of the ToK versions are placed on display it checks off both places in the checklist.
Solution- ??? If you don't know either maybe ask in LotD discord.
Lunar weapons - you know about this
Treasure hunt map III (for the library). This item is supposed to spawn in the bannered mare in whiterun. I was not able to locate it even when I turned off collision and teleported to it. I believe that it is supposed to be in a cupboard that was disabled by the bannered mare rework. Either that or it spawned on the roof for me and slid off into the abyss and then my position console commands don't do what I think they do.
Various hall of oddities items are placed inside of objects or buried underground:
1-Gold model ship(obtainable) is mostly inside a mead barrel in dragonsreach. (skyrim's unique treasures XX0064D3)
2-Jeweled horn(obtainable) is 100% inside of a dresser in Arcadia's cauldron but is still obtainable if the player looks at different angles. (skyrim's unique treasures XX005499)
3-Odahviing statue(unobtainable)- the chest containing it is buried underground at karthspire camp in a large stone platform (skyrim's unique treasures XX00F732)
4-Angel of death(unobtainable)- It is buried underground in lost valkygg (badgremlin's collection FEXXX807)
Cyrodilic brandy- Apothecary renamed this item colovian brandy and changed the model. It still works normally and has the TCC icon (with a different formID than normal colovian brandy). When you place it in the museum it transforms back into cyrodilic brandy with the correct model. More of a source of confusion than anything.
Saints and seducers extended cut causes 4 museum items to be unobtainable. 3 are fairly easy fixes.
1- jygallag sword(0500083B)- You can't loot thoron's body so that is not an option. Recommend placing it in the root nexus near thoron's helmet. An easier solution is to place it back in pelagius' mind where the original version went before saints and seducers. Edit: option 3- give jyggalag a copy in Vigilant. You have the opportunity to fight him in act 4 in coldharbour.
2- spell tome: conjure dark seducer archer- recommend adding it (05000B0C) to LList (31283035). This will give the ambersmith a ~82% chance to sell it along with the warrior tome that he sells normally.
3- spell tome: conjure golden saint archer- recommend adding it (05000AF0) to LList (31283033). This will give the ambersmith a ~82% chance to sell it along with the warrior tome that he sells normally.
4- root dungeon display. This one is difficult because the quest that is supposed to make it display is removed while S&S extended cut is installed. When the hall of wonders is entered a script is run that checks whether an objective is completed in the removed quest (entering the root dungeon in solitude sewers). You can trick it by using 'setobjectivecompleted ccBGSSSE025_QuestB 20 1' and then entering the hall of wonders to make it spawn. I don't know if there is a non-script solution that can make that happen automatically during one of S&S extended's quests but if you can find one (or write or edit a script) it will resolve that display.
*Note for me mod 05 is creation club saint's and seducers and mod 31 is S&S extended cut.
*Note There are 3 duplicate items that work correctly - keening, sunder, and wraithguard (one verison removed from LotD and another added by Tools of Kagrenac). When either of the ToK versions are placed on display it checks off both places in the checklist.
Solution- ??? If you don't know either maybe ask in LotD discord.
Lunar weapons - you know about this
Treasure hunt map III (for the library). This item is supposed to spawn in the bannered mare in whiterun. I was not able to locate it even when I turned off collision and teleported to it. I believe that it is supposed to be in a cupboard that was disabled by the bannered mare rework. Either that or it spawned on the roof for me and slid off into the abyss and then my position console commands don't do what I think they do.
Various hall of oddities items are placed inside of objects or buried underground: 1-Gold model ship(obtainable) is mostly inside a mead barrel in dragonsreach. (skyrim's unique treasures XX0064D3) 2-Jeweled horn(obtainable) is 100% inside of a dresser in Arcadia's cauldron but is still obtainable if the player looks at different angles. (skyrim's unique treasures XX005499) 3-Odahviing statue(unobtainable)- the chest containing it is buried underground at karthspire camp in a large stone platform (skyrim's unique treasures XX00F732) 4-Angel of death(unobtainable)- It is buried underground in lost valkygg (badgremlin's collection FEXXX807)
Cyrodilic brandy- Apothecary renamed this item colovian brandy and changed the model. It still works normally and has the TCC icon (with a different formID than normal colovian brandy). When you place it in the museum it transforms back into cyrodilic brandy with the correct model. More of a source of confusion than anything.
Saints and seducers extended cut causes 4 museum items to be unobtainable. 3 are fairly easy fixes. 1- jygallag sword(0500083B)- You can't loot thoron's body so that is not an option. Recommend placing it in the root nexus near thoron's helmet. An easier solution is to place it back in pelagius' mind where the original version went before saints and seducers. Edit: option 3- give jyggalag a copy in Vigilant. You have the opportunity to fight him in act 4 in coldharbour. 2- spell tome: conjure dark seducer archer- recommend adding it (05000B0C) to LList (31283035). This will give the ambersmith a ~82% chance to sell it along with the warrior tome that he sells normally. 3- spell tome: conjure golden saint archer- recommend adding it (05000AF0) to LList (31283033). This will give the ambersmith a ~82% chance to sell it along with the warrior tome that he sells normally. 4- root dungeon display. This one is difficult because the quest that is supposed to make it display is removed while S&S extended cut is installed. When the hall of wonders is entered a script is run that checks whether an objective is completed in the removed quest (entering the root dungeon in solitude sewers). You can trick it by using 'setobjectivecompleted ccBGSSSE025_QuestB 20 1' and then entering the hall of wonders to make it spawn. I don't know if there is a non-script solution that can make that happen automatically during one of S&S extended's quests but if you can find one (or write or edit a script) it will resolve that display. *Note for me mod 05 is creation club saint's and seducers and mod 31 is S&S extended cut.