A coil can "act up", especially once it gets hot, but once it's fried, it stays fried. I guess I haven't heard of Bonnies with a coil failure but it's a known classic triple problem. Why doesn't the dealer swap in a new coil to test it? There is no way they should keep your ride for 7 WEEKS. Maybe they are using it as a loaner bike

Get on their case, as nicely as you can and maybe find another dealer. A bad ignition pickup can cause spark problem, but I honestly know little about Bonnies and I'm not afraid to admit it.