I had a problem with the Euro/GBP exchange rate not updating when I used the Euro symble. I've replaed it with the word Euro, which I'm hoping will work.
I think you'll need to do the same for the pdf invoices.
Have you considered 'Not Branding'
So your biz A clients & your biz B clients do not get any branding, just something generic like:
'Client Support' rather than Brand A or B
Cheap & easy, even if not ideal.