I know this thread is old, but I find myself reading it today because I did the dumb thing of forgetting to clamp my lines before I flushed my heads.
2 things to remedy this problem:
1: Go into the EFI control screen and into "Parameters" and click the "Turn of Ink Fill Warning" box and hit "OK". You might have to do this a few times to get it to reset. If this doesn't work, do #2.
2. With the power COMPLETELY OFF, go to the back of your print carriage, and locate the overflow tanks, kind of right in the middle of the carriage. The one on the left is for the whites, the one on the right is for color. Pinch off the tube with your clamp, unscrew the cap, attach your syringe, unclamp the tube, and pull out any ink. Clamp off the line again, remove your syringe, pop the cap back on. Then, turn the printer back on again. You should hear a vibrating noise and that's the tanks resetting themselves. If the warnings are still on your screen, go through #1 again until they turn off.
This is how I fixed my problem. I hope this helps anyone else who is searching for a solution to this.