She knew before anyone could tell her, before anyone realized that it was actually Chakotay behind the strange behaviors of the crew. She knew whose memory pattern had been showing up in tests done by the doctor.
She could feel him, as sure as if he was there in solid, bodily form.
No one asked, and she did not tell.
And when it was over, she snuck into sickbay, and gave him her best lopsided smile.
“I knew it was you,” she whispered.