How will flagyl affect birth control pills when you have had sex the day before taking them?

Not a big concern: You are right that antibiotics can decrease the efficacy of birth control. However Flagyl is not one of the more worrisome antibiotics, and the effect would usually be after taking antibiotics. If you had sex before starting them, then it's not really a concern. Once you've started the antibiotics you should use a backup method until two weeks after finishing them. Good luck!