If you look at voice 2, the accidentals are written as if the key is in E flat, which is the sounding pitch. If you switch to Concert pitch, everything is okay, but in transposing pitch, which is B flat, the accidentals are not correct.
Anything I can do other than changing everything manually?
No, at the moment there’s nothing you can do except fix up the accidentals manually. This is a problem that we know about and which we will try to fix in the next major cycle.