Invoices sync into Sage 50 Canada with the default Payment Method that is set at the vendor level in Sage 50.
In the options tab of vendor card in Sage 50, you can find the Default Payment Method.
Pay later is the default if this setting was never adjusted previously.
If you've set your Sage 50 CA to import payments which will be submitted for approval and released in SageAPA. Make sure the Default Payment Method hasn't changed on the vendors you've onboarded for Direct Debit.