A lot of my comics are hand-drawn, and hand-coloured with Copic markers. Copic markers are a joy to use, and they look freaking amazing, especially in person.
They never look the same once scanned, but I just don’t really mind this most of the time. I think a bit of colour variation looks good. I do a few simple things to clean the image up and bring out the colour a bit, and bam. Comic looks good. I’m happy. The problem is the scanner sometimes just doesn’t pick up on the marker colour at all, or the contrast will be way off. My scanner has big problems with red. And… I love red.
This is a photo of Submameen! Part 6.

Let’s see that up close.

But what happens when I scan this and do the couple of simple colour alterations I normally do?

Oh no! Too saturated. The two colours in the background which are so distinct in person blend too much. I just can’t fix it. Time to rescan and toy with the ‘red’ settings in my scanner’s settings.

Better! I managed to pull that sweeping red colour out, and the two colours are more distinct. I can do something with this now.
But I’m unhappy with how muddy it looks now. I prefer the way the foreground came out in the previous scan. I don’t like this blue edge that has appeared in the linework.
What I decide to do is take both images and put them together. So now I have two layers, the older scan with the newer scan on top. They match up almost perfectly, so no problem there. I leave the top layer just a little transparent. Now, I can use the eraser tool to get rid of the new foreground, leaving the older one to show through.

See over on the right hand side? I’ve erased some of the top layer. It already looks much better. I’m happier with this colour.

See? There’s a stripe erased down his hat, and across the bridge. It looks better anyway because with only one layer, the linework is nice and sharp.
It’s a bit of a process because I have to do the edges carefully. It’s not so bad though - the images were already similar enough that a bit of the old BG showing through isn’t really noticable.
I decide in the end to erase not only the bridge-keeping dude in the foreground, but also most of Submameen, and the majority of the text bubbles (which look sharper and easier to read on the old scan). I also darken the gamma just a tad to give it a little more punch. I also leave just a little of the darker patches on the right-hand side of the hat and his back, because I like the extra definition that leaves as a shadow.
It ends up looking like this.

Which I am pretty happy with!
See the comparison between the first scan, second scan and the final product.

I am pleased with that.