Need Help Cyan/Black missing after running out of ink/change

You can try two powerful head cleanings to solve the problem. If not, you have to do the syringe method.

The syringe method usually works perfectly but as always, you have to be careful. I recommend you pulling ink with a 50ml syringe. I have a FJ-540 but I see that the your model doesn't differ too much.
You have to turn off the printer and then open the cover of the head section. You have to be sure that the heads are touching the capping section (there is a sort of wrench, a metal cylinder you insert in a hole under the main head section). Then you have to look for the tubes that goes from the black/cyan capping to the pumps. Connect it to your syringe and pull really smoothly (or you can break the dumpers). Ink should start filling the syringe. With 10ml of ink, it should be fine.

 

The ink lines probably just have some air in them from the empty cartridge. A couple strong cleanings should bring it back into the head but if it doesn't it is a sign that your cap tops or pump are not working at 100% efficiency.