If you are using WooCommerce PayPal Pro Payment Gateway on multiple websites you might experience “Duplicate Invoice ID Supplied” error.
There are really two ways how you can solve that problem.

1st – Modify your PayPal settings (not the best option).
2nd – Add unique “invoice prefix” (best option).

Solve Duplicate Invoice ID supplied Error by changing your PayPal Settings

In order for you to be able to accept multiple payments for the same invoice you need to turn that setting on in your PayPal account.

To do so go to:
Account Settings

Payment Preferences

Click “Update” next to block payments

Select “No” under Block accidental payments: You may prevent accidental payments by blocking duplicate invoice IDs

Done! Now you can accept multiple payments for the same invoice.

Add unique “invoice prefix” (Better Option)

Now, the option that we suggest is adding a “unique invoice prefix” for each of the websites that you are using WooCommerce PayPal Pro Payment Gateway on.

To do so go to “Plugin Editor”: in your WordPress Admin Menu

• Select WooCommerce PayPal Pro from the dropdown
• Select the file woo-paypal-pro-gateway-class.php
• Scroll down to the follow line (line number around 406) that has the following 'INVNUM' => apply_filters( 'wcpprog_invnum_woo_order_number', $this->order->get_order_number() ),
• And change it to the following: 'INVNUM' => "Your-Unique-Prefix-Here" . $this->order->get_order_number(),
• IMPORTANT! DO NOT USE ANY SPACES OR SPECIAL CHARACTERS IN YOUR INVOICE PREFIX

Done! Now your invoice will have custom invoice prefix and you no longer should be getting Duplicate Invoice ID Error.