You’re completely fine. You’re protected after 7 full days of taking it correctly ^ perfect use as stated above. Most combined pills have a 24 hour window in which to take a pill, as in if you’re due to take it at 9pm Tuesday then Tuesday’s pill isn’t counted as missed until you don’t take it by 9pm Wednesday. Even then you can safely miss a pill anywhere in the pack on most combined pills without your protection being affected. Taking it 9.30pm or 2am, or 3pm or 6pm has no effect on your protection, but some people find they are sensitive to taking it inconsistently and are prone to experiencing unwanted side effects if they take the pill at different times.
You are either fully protected on the pill or not protected at all, there is no more or less protected. The 99.9% effectiveness thing is how effective the pill is statistically at preventing pregnancy over a year of perfect use (for legal reasons they cannot say it’s 100% effective), not that you’re 99.9% protected at any given time.