Lotte knows this, and it’s possible that Maxine is informed of what’s going on during her kidnapping, but Craig doesn’t.
Being John Malkovich is ultimately about a truly strange love triangle formed between Craig, Lotte, and Maxine, and as strange as their relationship is from the get-go – with Craig being married to Lotte and then falling in love with Maxine, only to then learn that Lotte is in love with Maxine as well – things end in an even more bizarre place.
As explained during the second act of the movie, Dr. Lester and his group need to enter the Malkovich door before midnight on his 44th birthday, with the given reason being that entering the door after that point in time would result in the collective being diverted to a “larval vessel” and getting absorbed.