I think the only way that it could "mess up" your ovulation is if you've been given too strong of a dose, which could push you from being hypothyroid (not enough thyroid hormones) to being HYPERthyroid (too much thyroid hormones).
If your dose is titrated correctly (i.e., the "ideal" TSH level for women trying to conceive is between 1 and 2, NOT the broader ranges that qualify as generally "normal"), then you should be fine.
Regardless of whether or not you're on fertility meds of any sort, you NEED to make sure that your thyroid levels are controlled - ESPECIALLY when you get pregnant. Uncontrolled (or not optimally controlled) thyroid function can cause a lot of issues with pregnancy (including loss, decreased fetal brain development, etc). Once you GET pregnant, you will want to have your thyroid levels checked regularly (at least once per trimester).
HTH,
dk
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