Hey, @KIm_73. Welcome to the Community, and thanks for your question!
The payment gateway(s) on your store are actually controlled from within your Shopify admin, not your theme. As long as AfterPay is a gateway that is available to use in your region (you can check on that here), once it’s enabled it will continue to be a payment option on your store even if you change themes.
Therefore, it sounds like it must have been disabled on your account. To add it back again please go to ‘Settings > Payments’ from your Shopify admin. Scroll down to the Alternative Payments section, and click on the Choose alternative payment button. Select AfterPay and enter your Merchant ID and Secret Key that you obtained from AfterPay directly to activate it in your store. These steps are also found in the Help Doc for Alternative Payments.
Let me know if this helps!