In the first movie, Barbara's character was changed from one of Susan's teachers to the Doctor's elder grand-daughter. The problem with this is that her character didn't appear in the serial the second movie is based upon, so it does leave the audience wondering where she vanished to.
Maybe I'm misreading your post but Barbara is most definitely in the original televison version of this story. Neither Roy Castle or Jenny Linden wanted to do the second film so they created Tom and Louise, rather than recast.
Yes... so in this story, where is Barbara is what he was asking.
I guess you'd assume that they managed to take Ian home to his original time, unlike the original series, and Barbara stayed with him. Then they picked up Louise, and we see them meet Tom.
Everyone always blames Ian (Roy Castle) for "accidentally" sending the TARDIS into the timestream. It wasn't his fault! It was Barbara's! SHE's the one who pushed him backwards onto the lever without watching what she was doing...