Are you sure it can't be done? I just tried a short clip:
This:
!NoteWorthyComposerClip(2.0,Single)
|TimeSig|Signature:6/8
|Note|Dur:8th|Pos:0
|Note|Dur:8th|Pos:0
|Note|Dur:8th|Pos:0
|Note|Dur:8th|Pos:0
|Note|Dur:8th|Pos:0
|Note|Dur:8th|Pos:0
|Bar
|Note|Dur:4th|Pos:0
|Note|Dur:8th|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:8th|Pos:0
|Bar
|Note|Dur:Half,Dotted|Pos:0
|Bar
|Note|Dur:4th|Pos:0
|Note|Dur:8th|Pos:0
|Note|Dur:8th|Pos:0
|Note|Dur:8th|Pos:0
|Note|Dur:8th|Pos:0
|Bar
|Note|Dur:8th|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:8th|Pos:0
|Note|Dur:4th|Pos:0
|Bar
!NoteWorthyComposerClip-End
to this
!NoteWorthyComposerClip(2.0,Single)
|TimeSig|Signature:6/8
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:0
|Bar
|Note|Dur:Half|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:Half|Pos:0
|Note|Dur:4th|Pos:0
|Bar
|Note|Dur:Whole,Dotted|Pos:0
|Bar
|Note|Dur:Half|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:0
|Bar
|Note|Dur:4th|Pos:0
|Note|Dur:Half|Pos:0
|Note|Dur:4th|Pos:0
|Note|Dur:Half|Pos:0
|Bar
!NoteWorthyComposerClip-End
was simply a matter of highlighting the entire staff and pressing the plus key, then changing the key signature.
I then opened a complicated clarinet/piano score of 180 bars and did the same thing. Then I tried a 182 bar, 21 staff band score, and did the same. It seems to work although I'd be careful with anything "global" like this.
You do have to do each staff separately.