Switching site locations would allow them to take down the primary site for maintenance, upgrades, etc. There are also cell and other public safety and business transmitters very near the primary EDACS site, I don't know if they would switch sites if there is work being done on those antennas. Also, of course, in case the primary site fails they have a full backup ready to go.
Switching sites certainly would impact signal quality in a large part of town, which is why they use the primary site most of the time. There wouldn't necessarily have to be anything else going on to cause the problems you describe.
Do you know what areas were most impacted? I would expect switching to the alternate site would improve service in the Kingston area, be negligible in Kendall Park and Monmouth Junction but with more noticable degradation in buildings in these areas, and possibly hurt service in Deans and Dayton on out towards the turnpike.
Simulcasting would be nice but, I've heard, requires infrastructure upgrades or additional work of some kind to SB's current equipment. From one price tag I heard I believe it is more than just synchronizing the towers, though I don't know how much that would cost.
Jim