Hi Rukmni,
Clinical studies have not shown any interference between Alli and synthroid, the dosing recommendation stands of taking synthroid first thing in the morning at least 1 hour before any other food or medication.
Many people do choose to skip the breakfast dose of Alli in general since they are eating very low fat (5 grams of fat or less) during this meal and save the pills for higher fat meals.
With weight loss your thyroid levels may need to be rechecked and a dosage adjustment may be necessary.
Hope this helps.
Sophia De Monte RPh