GSTIN Invoicing

I think Consolidated invoice is possible, section to be check 

Keep it simple. Ask for separate invoices for respective GSTIN. ITC will not be available. Also monitor the value of gifts given to an employee since they can be treated as supply beyond threshold

You should ask for a separate invoice. Consolidated will also do but in that case you will have to follow the below process:
Suppose the consolidated bill is raised on Hyderabad. Then Hyderabad will raise an inovice against Bangalore unit for the value equivalent to the amount paid for 500 employees. Also it will raise an inovice to Pune unit for the value equivalent to the amount paid for 400 employees. These invoices will also have GST amount. So the units will be able to claim ITC on the basis of these invoices