ST Voyager "Demon":
DEMON KIM: We'd rather die than be alone. We deserve life.
JANEWAY: This silver blood that created you. It duplicated Harry without killing him. So you don't need our bodies, only samples of DNA. Release Voyager and I'll speak to my crew. And if they're willing, I'll let you duplicate the rest of us.
TUVOK [OC]: Bridge to Janeway. We've stopped, Captain. We're no longer submerging.
JANEWAY: Understood. We're getting out of here, Tuvok, but first assemble the crew in Cargo Bay one
So they know that they are not the actual crew and cut a deal for the DNA of the real crew, they also cannot breathe oxygen/nitrogen air.
ST Voyager "Oblivion":
CHAKOTAY: That wasn't B'Elanna. It was a duplicate. A biomimetic copy.
TUVOK: We are all duplicates. None of us are real.
(Later, Janeway is looking at a flask of silver liquid.)
EMH: Behold the primordial soup.
JANEWAY: That's what created us?
CHAKOTAY: Not just us. The entire ship is composed of the same material.
EMH: It's a biomimetic compound that duplicated the crew's molecular structure so precisely that I would never have detected it, if I hadn't known what to look for.
JANEWAY: I was born on Earth in Indiana. I remember growing up there. I remember graduating from the Academy. I have no memory of being a copy. Somehow, after the real Voyager left, we began to forget we were duplicates.
EMH: Apparently, the original Kathryn Janeway's memories were duplicated as well.
CHAKOTAY: Eventually, we assumed their lives and set a course for Earth.
I was really confused by this episode.
How could the crew have forgotten that they were duplicates?
(Please don't make your answer what I already stated that Chakotay said "somehow they forgot" that's not an answer that's the question. Also if you want to address how they adapted their lungs somehow, also unknown to anybody including the doctor whose memory shouldn't be affected and how they created an identical starship with all of the technology, computer memory, etc. in place that'd be helpful as well and plays into the question.)