ktroyh

I was recently doing some work on my son's 1991 Justy and while under the dash I saw the green connectors and the black connectors to not be connected. I knew he had problems with a couple of systems on the car and like an idiot I thought that is why those don't work properly so I connected them. He had no check engine light s prior to this. I now know they are for checking engine codes etc. My issue now is I have a flashing check engine light when there are no check code wires connected. Everything I have read states that I should get that with no codes and the black wires connected. Does the check engine flash when there is a problem or just stay on? Can anyone help me with this? Thanks,