Pull codes first, see what the car thinks might be wrong. Any LEDs or electronics installed?
Sounds more like a dying battery to me. Yeah, it sounds a bit early, but not unlikely. The dealership shouldn't have had to disconnect the battery to flash any modules that I know of. BUT, it is worth checking to make sure that no cabling is loose, that the terminals are firmly connected to the battery. Get it load tested with a digital load tester, that will tell you for sure. Because once you ran the car on the highway, it should have been charged up just fine. Check carefully for leaks from the battery also, hopefully the case hasn't busted. Sometimes when a reflash is done, it can mess up the battery management system, though that is rare.
There is a small possibility that the alternator is going bad, or that the sensor at the battery (used for the battery management system) is going bad. Check the voltage of the battery with everything turned off (no load). Should be around 12.5-12.6V. With the engine running and revving at around 2,000 rpm, it should be around 14.5V, no greater than 15V. That is a quick check on battery/alternator. If those are good, the starter is worth considering. That is an extremely rare part to go bad on the SHO, but I have noted that the frequency is increasing (though still rare) for older MY Edge vehicles.