Out of box, majority of Control Documents have been designed in a way, that report for 1 Invoice/Customer is printed at a time. And it is supposed to save one PDF per Invoice/Customer.
If you will open this report in VS designer, you will find the fact that Header has no relationship with Footer.
There are only DataSources, bringing data from RDP and displaying those on report.
In short, one PDF is saved per Invoice/Customer, because of design.
There is no support in standard AX, for your requirement. It was developed in this way, because this is general practice to print a separate file for each invoice/customer.
Now solution to your issue can be any of following two choices
1) Redesign/ create a new report that will support to print multiple invoices for different customers, once, Grouped by CustomerId & InvoiceId
This can be done as demonstrated here
your header and body of report will share a common parameter or you will not include any report header, instead you will manage your report header, in a way that all data(header+body) will be displayed in same tablix of SSRS and you can put few white lines or empty rows between header information and body
2) Generate multiple invoice & save all PDF files at any specific location/folder, now combine multiple PDF with using any software
If I were in your shoes, I would prefer #1 approach. as it will be one time solution for me and lifetime I can use that report, instead of going through practice of #2, where any 3rd party software may not give needed results 100% correct