Well, I'll preface this by saying faces are asymmetrical, so if it is just a little different, you should be fine.
With that out of the way, you wouldn't have been bothered by a little asymmetry in your drawing, so I susprect that when flipped it looked messed up. Honestly, I have that problem quite often, and to me, it's trial and error until a kinda "build" a face that looks ok when flipped. You could try to copy and flip the eye if the angle allows it (it's usualy the eyes that mess the face up the most), but that's not always possible.
My advice is to flip the drawing constantly while you are drawing it. Don't draw the whole face and only then flip it, if you're insecure. Flip it as many times as you need during the process, so you can see what makes the face asymmetrical and fix it as soon as possible.