Surely it can’t be the trifid cipher, as it was invented in 1902/1901/1893? (depending on sources) The story takes place in 1851, so unless time-travel exists (which is implied in the BOSS case file archives), it shouldn’t be encoded using the trifid cipher.
That being said, I still have no clue what the cipher is. my brain has turned to mush.
send help.
-R