Progestin causing af to go rogue???

Hi everyone. I'm on progestin (200 mg 2x daily) for my lutal phase defect. I'm supposed to keep taking it until af starts or I get a positive pregnancy test. Will it cause me to not have an af while I'm on it??? My Obgyn said it won't but I'm 2 days late?!!!! (Bfn two days ago - I had baddddd cramps that day too). I'm only 12 dpo (I ovulate cd 22)