I know it's a bit evil, but have you considered using msgctxt for actual IDs instead? msgmerge (and all the other gettext tools) should work with that correctly in that case. Of course, I can imagine you don't want to change the set-up once again, so I'll think by Monday what can we do to help you out that doesn't take too much time for us (ideally, we'd fix the underlying problem).
I know it's a bit evil, but have you considered using msgctxt for actual IDs instead? msgmerge (and all the other gettext tools) should work with that correctly in that case. Of course, I can imagine you don't want to change the set-up once again, so I'll think by Monday what can we do to help you out that doesn't take too much time for us (ideally, we'd fix the underlying problem).