After i collected one of the containers and get the knowledge scroll from it, it is disappeared after i restart the game. No error, crash, what so ever. Just vanished.

Had you gone into creative at any point during thay previous session? It kills fragment advancements and items from that session, if so, to prevent creative unlocking.

Same issue on my side. I got a knowledge scroll in a world, where cheats are disabled and I haven't gone into creative. If I read the scroll the knowledge is available in the tome, if I save and reopen the world the knowledge is still there, but if I reload the modpack, the knowledge is gone.

Tried it with only Astralsorcery 1.10.3, Baubles and JEI installed.

@VictorScrooge @wamc2017 please confirm that the directory being written to has write permissions the whole way down, please.

Yeah, there's definitely write access to the file. I checked with NBTExplorer:

Seems to be an issue with loading the file, when I restart the instance...

THAT could be it