I might sound like a dumbass right now, but I took Linda to the incubation tank similar to the one we woke up in, and we thought about taking her there, but when I leave the science lab and re-enter, Linda wasn't in her usual spot, but becomes my companion instead. Leaving and re-entering, also rechecking the area many times, she still follows me around in the science lab. How can I progress from this point?
oh nevermind. Turns out it was a glitch where I invited Linda to the dungeon, then accidentally exits without freeing her, so she somehow still becomes my companion in the science lab. Also she's always naked now, so yay.
as for my original matter, I fixed it by visiting the dungeon again and freeing Linda, she got back to her usual spot, without any clothes on.