well, i dont know why people get scared of going back to nepal to get H1B stamp.  actually it is lot easier there than we think from here.  i did that and so many people that i know did that.  i also had gap and went back to nepal, stayed home and got stamped at us embassy.  no problem at all.  no one applying for H1B had any problem the day i took my interview. 

anyways, since she did not do that and worked while on F2, it can be a problem now.  however, what i wwould do is, i would not take pay stub of those months with me and her employer can also help her by writing a memo for her to present at embassy.  a lot of people work on paycheck while on f1, so i am guessing this is similar situation.  she was never out of status, so this should nto be problem.