Can I invoice based on contract percentage instead of time and expenses?

Yes, you can. When creating an invoice from the Invoice Batch screen, you can open the More menu and select Show/Hide Columns > % Complete. Enter the percentage of completion for the project in this column, say 50%. It calculates the invoice value as a percentage on the contract amount. Process the invoice and it will reflect the percentage set of the contract amount. Check this article on the different billing methods available in CORE. 

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