Oo, birth control can definitely affect your cycle, some of us moms noticed na parang mas maikli or mas matagal ang period after missing pills din, lalo na if you stopped takin them suddenly! But honestly, given na negative ang PT mo and you had contact lang 2 days after a 3-day period, ang risk is quite low, pero since you're worried and may health concerns ka with another pregnancy, best talaga to check with your doctor, especially if cycle mo is still off kasi they can properly assess kung hormonal lang or may iba. Don't stress too much muna, maraming reasons bakit pwedeng mag-shift ang cycle besides pregnancy, pero peace of mind lang talaga makukuha mo from your OB. Sending you strength, momsh!