This happened to me a lot, but there’s actually a way to save it with photoshop! If the sketch is lighter than the lineart, that is. This is how I do it:

When that happens, I flatten the whole thing.

And then click on Image > Adjustment > Levels

Then click on the darkest shade of sketch you want to get rid of. In this case, the parts I circled below.

Press OK, and there you go! 

A clean and workable lineart!

I hope this helps? :D

SUDDENLY I AM STRUCK BY THIS HUGE EPIPHANY
THEN I SLAP MYSELF FOR NOT THINKING OF IT EARLIER

I… oh.. 

reblogging this again because I need it for homework! JOLLY GOOD