Oh, right, for the advice lines; I didn't notice the issue because I never used them after the first time I ever played BG2.
Hm, those will definitely have to be rewritten for BGEE, EET and IWDEE, yes. From what I saw so far, EET uses BGxxxx for the BG1 areas, while keeping the xxxx code the same as in BG1. I also saw some BDxxxx areas (which I think are from SoD) and OHxxxx areas (Black Pits?). I am less sure how they handle chapters, though. I am curious now if they changed the area naming scheme for regular BGT as well, in which case all of that will need to be rewritten anyway.
A workaround for now would be to disable the advice dialog option in BGEE, EET and IWDEE; it will take some time to work through.