In prep for my FET, I was on the patch only (4 of them changed every other day) and my levels were still too low, so I added estradiol vaginally 2 times daily. My nurse said that for 50% of people the patch alone is enough. I never did any orally and my lining was beautiful.
i really don't think that missing a pill and being late on one would affect anything when you've got the patch and vaginal ones. Fx that your lining is great and you can do your transfer! If you do happen to get cancelled, I don't think it would be because of your illness. Good luck!!!