Hi, and thanks for your medical question on eHealth forum!
Yes, prolonged use of birth control pills can cause discharge, spotting, irregular periods or complete stoppage of periods. This could have happened in your case. This does not make the pills less effective, unless you have missed a pill/pills in between. Take a blood test to estimate HCG levels as a confirmatory test for pregnancy.
Since a confirmed diagnosis cannot be given on net please consult your gynecologist regarding this. Hope this helps. Take care!