If you wish to collect payments for invoices that were issued while payments were disabled on your proposal, you can definitely do so manually.
Note: If your client doesn't have their payment details in PI yet, you will need to update their payment details first. Check out this article to learn how. You can skip this if they have entered their payment details or if they have a previous proposal with you with payments enabled.
Here's how to collect payment for invoices that have skipped collection:
First, let's re-enable payments. Open the proposal you need to work on and go straight into the Invoices & Payments tab then click on Enable payments. Choose which payment details to use or add a new one and click Save. Learn more about managing your client's payment details here.
Then click on the cog next to the invoice you wish to collect payment for and click Schedule Payment Collection. Choose whether you collect the payment today or a custom date in the future.