If your invoice is paid via Stripe, you need to turn off this setting or else the record won't be correct.
After you connect your Stripe account, you need to edit the payment method and delete the Account.
Settings > Payment methods > click on the edit icon next to Stripe
Then just delete the Account and save, see the GIF above.
If you don't take this step, you'll have to void the payment transaction in Stripe to release the Invoice so that you can reconcile it in your checking account.