Instrument not transposing correctly

I have written a score for two transposing instruments (bass flute and bass clarinet) which I have written at concert pitch. I now want to change the full score to a performing score (no parts), i.e. with transpositions. I’ve indicated in the Layout Options/ Players that the layouts are Transposing layouts. However, only the bass clarinet part is adjusted, the bass flute retains the same concert pitch (i.e. without octave transposition).
Any help appreciated.

I’m not an expert on bass flute transposition, but is this one of those situations where sometimes an octave clef is used and sometimes not? There’s an option on the Clefs page of Notation Options for whether or not octave clefs affect the octave at which the notation is displayed.

AFAIK bass flute isn’t a “transposing instrument,” it is notated an octave above the sounding pitch, similar to contrabass, or (an octave in the opposite direction) piccolo.

The fingerings for the concert flute, alto flute, and bass flute are the same, so players want the notation to be consistent with the fingering.

(The alto flute is a transposing instrument, because the concert flute fingering gives sounding pitches a fourth lower.)

Thanks for that.
For some reason I can’t select the bass flute’s clef (in Write or Engrave). I can select the clarinet’s. Any idea what I’m doing wrong?

You can only select a clef if you’ve created an explicit clef in the staff. If the clef isn’t selectable, it’s just the default clef defined by the instrument itself. You can create a clef change at the start of the flow if you wish, of course.

Ah, now I understand. Thanks for that.