You can use the append PDF option to combine multiple PDF files into one. If you need to keep each pdf as a separate PDFs you'll need to look at a PDF plugin that will allow you to attach multiple pdfs.
Just thought of another thing that might be better. Zip all of the PDFs into one zip and then email the zip.
Create a linked PDF table - four fields
ID from invoice
containerA for sent invoice
containerB for accountants invoice
create the PDF, store it and send to customer, create PDF and store for accountant
When time comes to send batch to accountant, a bit of plugin magic and concatenate all the PDF files into one and email it.
I would be doing it with iText and ScriptMaster, but others are available, and I would be doing it direct from containers to one finished file on the hard drive...
If you don't want to mess with a plugin. Create a looping script that names the PDF and creates your PDFs into one folder. Zip the folder and attach it to the email. Fairly easy to do. I would rather send multiple files as a zip instead of sending multiple files in one email.