I have drawn a pattern on the computer and then printed it out on A4. I would like to go over it using black pen, can I do this and then scan the finished piece into the computer while maintaining it's good quality? I'm not sure because the ink from the printer might prevent the black ink to prioritise during the scanning process. Does anyone know?
I'll offer a simpler solution. Go over it using a lightbox and whatever material will give you enough visibility to see your pattern. Mylar or Tracing Paper most likely. Scan the new sheet and do whatever you want with your print-out.
If you need the two combined it won't take much effort to switch the Blending Mode of your new scan to Multiply once its back on the computer.
You can do this, but be careful when you go over with a black pen. If you do this with attention and carefully and not applying a big pressure on the pen, everything will be fine.
If your pattern is in one color, you should print it with a laser printer and then scan in grayscale to avoid having issues with your black or at least be able to modify it easily. Inkjet are not the best for this since the ink tends to spread more on the paper and the edges of your pattern might be blurry.
Laser printer usually offer a very sharp result when the artwork is in one color and 100% density. It's also easier to work with a file at 100% density and then modify it later if you need to by using transparency or applying shade in Photoshop or Illustrator (or whatever software you'll use.)
You should also scan back at very high resolution like 600ppi, and if it's alright for your artwork (which you don't provide any sample of), you should convert it to lineart bitmap mode at 600ppi and more. It will print as sharp as a vector at 100% of its size.
If you have a color pattern, then you can use inkjet on a very high quality photo paper, and if you can. When you'll draw with you pen, you'll need to be careful when scanning it back; the rich blacks will need to be the same everywhere or this might be visible once printed back again! The color of the ink from the printer and from your retouching will certainly be different.