Did you have the two green connectors plugged together under the drivers side dash? That can make the CEL flash constantly as it activates a diagnostic mode for the ECU. It may have gone away if the wire you cut was from one of those connectors. The green plugs should be left disconnected, and if this is indeed what happened you probably cut the wrong wire as it should not have had any affect on the diagnostic connectors or the CEL.
I'd suggest getting some help from a shop or someone with more experience before you cut any more wires.
Oh, and if the car had a CEL from a catless downpipe with no "fix" installed the light would be on steadily, not flashing.