Hi @chrishardie
The issue you described, where a new payment method is not set as the default for a user account when entered for a Woo Subscription, seems to be more related to the Woo Subscriptions plugin rather than the WooCommerce Square plugin.
The Square plugin is primarily responsible for processing payments and saving the payment method, while the Woo Subscriptions plugin typically handles the default payment method for a user account.
However, to ensure a comprehensive solution, if you have a valid license for Woo Subscription with us, I’d recommend you open a support request for us to investigate further about your issue.
Meanwhile, I will be marking this thread as resolved since your concern would be best handled by our Happiness Engineers there.
Thank you for your understanding and cooperation.