I took a closer look at the non-saving of manually entered notes on the soloist track, and this has to be a bug.

I entered some soloist track notes in BIAB 2007 for Windows under Parallels, saved the file, closed it and reopened it - the notes I entered are always there and always play. Then I opened the same file under BIAB 2009 for Mac, the soloist track is empty and there's nothing to hear on playback. Re-opened again under Windows and could confirm that everything's still there, so it seems BIAB 2009 just isn't reading the file properly.

Then I typed one extra note in BIAB for Mac, in a place where I know there were no other notes. Saved that, re-opened it under Windows, and everything's vanished except that one extra note. Reopened it again under Mac, and again my one note had disappeared.