Which is correct:
1-I remember her working here during both her pregnancies.
2-I remember her working here when she was pregnant with both her children. (I am assuming that the children aren't twins.)
I vote for #1 in your original post.
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.