While I need multiple Invoice Auto Generation Numbers for my business I used a workaround which I will very basically describe below: 

1) We create a Workflow when an Invoice is created and we assign a custom function.

2) We disable the Zoho Books auto generation feature for the Invoices.

3) We create a new App in Zoho Creator with a single form which has as many fields as the auto generating numbers we need. So, its field stores the Invoice Number for the next Invoice in Zoho Books. 

4) Now we create a custom function in Zoho Books to do the following: 

• Fetch the next invoice number from Zoho Creator App. 
• Update the Invoice we just created with the above invoice number.
• Increase the Invoice Number by 1 and send the new value to Zoho Creator to store it for the next invoice.

This works for my business very good.