Pantoprazole and Tirosint?

Interactions between your drugs
Moderate
levothyroxine pantoprazole
Applies to: Tirosint (levothyroxine), pantoprazole

Taking levothyroxine with pantoprazole may interfere with the absorption of levothyroxine and reduce its effectiveness. Contact your doctor if you experience signs and symptoms of reduced thyroid function such as fatigue; sluggishness; constipation; depression; hoarseness; unexplained weight gain; sensitivity to cold; pale, dry skin; muscle aches, weakness, or tenderness; joint pain, stiffness, or swelling; heavier than normal menstruation periods; or brittle fingernails and hair. You may need a dose adjustment or more frequent monitoring by your doctor to safely use both medications. It is important to tell your doctor about all other medications you use, including vitamins and herbs. Do not stop using any medications without first talking to your doctor

Source: https://www.drugs.com/interactions-check.php?drug_list=1790-0,1463-3519

Pantoprazole belongs to the drug of PPI (Proton Pump Inhibitors).

https://www.drugs.com/pantoprazole.html

With regards to how you should take the PPI and the thyroid medication I strongly advice for you to ask your DR., when one pharmacist says one thing and another something else, well, in my case I do not like the guessing of which one is right or wrong, so as I mentioned ask your Dr..
As you have read from the interaction report Pantoprazole may interfere with the absorption of your thyroid medication and it may lose effectiveness.