I can't seem to determine whether or not the AC44C6Ms have new FDLs or not, but I suspect that they do, or completely upgraded and rebuilt ones. Whatever was cheaper... These conversions are expensive, up to half the cost of a new-build AC4400CW, as NS is expecting to get another 20+ years out of them.
The reasons behind these conversions are twofold. The first was to ensure that if Tier IV locomotives were unworkable there would be a supply of effectively new power. This was the reasoning behind the Dash-8.5CW program, and when they were successful and the rebuild program suffered still-unknown teething issues, NS killed the program and bought ET44ACs.
The Dash-9 series is when GE finally matched the quality of EMD, so they are getting the first major successful GE rebuild program. GEs have not been rebuilt in quantity in the past because of quality issues in the early years, and a differing philosophy than EMD. GEs are cheaper, but are much less backwards-compatible with earlier models than EMDs. Furthermore, GE has been much more protective of its parts supply. EMD willingly licensed more of its technology away, to the point where (via M-K/Wabtec) GE builds/built EMD 645s in Poland! GE, though, made sure that they were the only ones to sell their parts, and when they stop, most of the models needing them die. The remaining Dash-7s on Class Ones all were retired within a few months in 2007 because of this. With the Dash-9 line this is different, and BNSF is also rebuilding their earliest Dash-9s as AC power. The AC44C6M program is a major life-extension program somewhat similar to what NS has done with SD50s (SD40E) and SD60s (SD60E).
GE has apparently picked up an ex-NS GP38-2, rumored to be used as the Erie shop switcher. Not sure that I believe that!