Since the business is defined by the EIN, they still only file once per EIN, no matter how many locations they have.
The IRS says, "Generally, businesses need a new EIN when their ownership or structure has changed" ( Do You Need a New EIN?).
"An important part of figuring out how to open a second business location is the following IRS requirements. You do not need a new Employer Identification Number (EIN) for your new business location. But, if you are changing your business’s structure, you will need a new EIN for your entire business" ( ACA Reporter).