The bookshelf need to be added to the blacklist or you can't open them at all.

Might be compatibility issue?

I'm on 1.12.2

okay I tried reproducing it on flat world myself and it seems you are right, the chests that I mentioned before can be opened. Idk if that's because I use Chunk Pregenerator mod on my world before since I don't use Chunk Pregenerator on the flat world.

I tested it out with a new world without pregening and all the chests can be opened. I guess that's solved.

Also I found out chests from Recurrent Complex Structures also not replaced by Lootr chests, is there anyway I can force it to change? Sorry if it's going out of topic from the title mentioned, do I need to post a new issue for this?

Try enabling CONVERT_WORLDGEN_INVENTORIES. It will be more aggressive with that option enabled and convert any inventory in the world that contains items, that was not placed after worldgen.

Unfortunately I'm not sure I can do anything to prevent this automatically. Evidently the bookshelves are using loot tables and being picked up as a loot-based block. 1.12 doesn't have tags so it's hard to know what is a chest and what isn't.

I could however add them to the blacklist by default; what is their registry name?

I added this

ebwizardry:oak_bookshelf
ebwizardry:spruce_bookshelf
ebwizardry:birch_bookshelf
ebwizardry:jungle_bookshelf
ebwizardry:acacia_bookshelf
ebwizardry:dark_oak_bookshelf
tfspellpack:twilight_oak_bookshelf
tfspellpack:canopy_bookshelf
tfspellpack:mangrove_bookshelf
tfspellpack:darkwood_bookshelf
tfspellpack:timewood_bookshelf
tfspellpack:transwood_bookshelf
tfspellpack:minewood_bookshelf
tfspellpack:sortingwood_bookshelf

Also I added this

S:LOOT_MODID_BLACKLIST <
	iceandfire
	ebwizardry
	w_tweaks
 >

Since Ice and Fire, Electroblob's Wizardry, and Wizardry Tales behave the same when their chests turned into Lootr chests they cannot be opened, and If I break it will just return an empty chest. So that's the correct ways to blacklist a mod?

Since Ice and Fire, Electroblob's Wizardry, and Wizardry Tales behave the same when their chests turned into Lootr chests they cannot be opened

Okay, that is a bug. The chest should still be possible to open.

Do I need to provide any logs to help?

I don't need any logs, but could you quickly explain how I can find a naturally generated bookshelf/block from each of these mods? I've never played with any of them so that would speed up reproduction greatly.

Basically it just spawned in randomly, maybe it's easier to do it either in flat world while increase the spawn chance in the config files? Personally I never done that but when I fly around in creative they are quite easy to find.

Is this the type of chest that wouldn't open? It seemed to work for me. Perhaps a log would be helpful after all.

That works! I guess I'll close this, thank you so much for the quick response and the solution.