ECPs are only good to protect against one act of unprotected sex. They work by blocking ovulation, but only for a few days, so if you take them and have unprotected sex again afterward, you're significantly increasing your risk of pregnancy.
It will not have a long-term effect on your reproductive health. You may notice irregular bleeding patterns and your period may be early or late, but emergency contraception will not affect your fertility or become less effective over time. In fact, it will not even harm a pregnancy if you've already become pregnant.
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