Hey! Yes it will still be effective....please, please, please START SLOW! I am speaking from experience. You will have to build up your tolerance again. If it worked for you before, it will work again. Just be patient with it.

Good luck.

Thanks for the feedback.

Also, for how long will I experience the peeling and dryness from the benzoyl peroxide? It's discouraging

Thanks again. 

Even with daily make-up routine on which by far isn't highly recommended when in progress of clearing your acne, the regimen should still be effective however the process of your acne clearing up would take a little longer. The reason why it'll take longer is because you have other stuff put on your face other than the regimen alone which is another form of irritation on your skin. However I would recommend using primer on your face before putting on make-up to help your skin to be most likely protected from irritation of make-up.Take it from me, I usedmake-up while on regimen and I was able to clear up from it lol so yeah, here's another hope for you from me!