What to do if upsell is not working with Stripe even if I clicked the "Yes" button on the upsell page?
If you use Stripe (1CU) and everything works properly in "Test mode", but in "Live mode" you have the issue with the upsell orders, that's your case.
Your parent order payment comes through properly in "Live mode", but upsell payment fails in "Live mode" because you need to force HTTPS on your whole website and not only on checkout page. Or alternatively you can just force in on your upsell pages and checkout page. That will fix the issue.
Because if the upsell page is not served over HTTPS, then Stripe payment for the upsell in "Live mode" fails, because Stripe is declining all the real payment requests made from the insecure pages.