If you choose Mysterian in the second cycle and haven't done the main part of Styx yet, Lilim teleports you directly to the end of it, with the lower part of the crypt staying blocked off. If you got the key in the Crypt it's not something you'd have to worry about, and in whatever case getting all the keys is something that requires having both the lower Crypt and the main body of Styx accessible.
There is the fan discord linked down below that has some documentation in it, but the link's expired at this point.