Setting is basically an Earthlike planet that is not Earth. The tech level is a mix of now and future =- they have a portable wormhole that they use to get across the continent in a hurry, for example, but they may never have developed the internal combustion engine unless I need them to for this event. There are some other minor differences, but I don't think they matter for the purpose of this question.
This civilisation has three major units of mobile technology - airships, boats, and walking cities. The airships and boats are piloted craft; the walking cities are programmed with a set of parameters so that they don't try to walk into the ocean or up a mountain and let go from there. The airships are a bit more like directed, efficient dirigbles with airplane instrumentation. (Because reasons. Explodey reasons.) I need to crash all the boats and airships at the same time and leave the walking cities alone. I think the easiest way to do this is to use an EMP burst to take out the instruments that the boats and airships are using, but I don't know if that even makes sense. Obviously, I have a lot of fudge room here, but I need to crash everything over a continent roughly the size of Eurasia. There's not a lot up there, but it's pretty spread out.
From the viewpoint of my characters, the civilisation that did this had science and magic both, because they don't understand the level of science the civilisation had achieved. The result of this event is that the continent was thrown back to the dark ages and they haven't recovered because the Big Bad doesn't want the world to develop technologically to the point of having a war like that again, and has the ability to stop that development happening. So they do not understand what actually happened. In other words, I could have a degree of actual magic, but I would rather science this shit if possible.
My understanding is that electromagnetic radiation is my special friend here. Wikipedia tells me that of the four ways to generate an EMP burst, which are electric field, magnetic field, electromagnetic radiation, and electrical conduction, only electromagnetic radiation acts over distance. I need to know how I could trigger that, and, even better, how I could get this civilisation to do it to itself. I cannot have the sun go mad and CME my planet, and I cannot have this be enemy action. I would like not to have this be nuclear EMP, given that my main characters are all walking into the city that did this, and it's only two thousand years later and I have no plans to kill them all as quickly as I imagine that would. I don't need to crash everything simultaneously, but I would like it to all happen on the same day.
1) Could I have all of these vessels in contact with satellites that are connected to their home city and have my EMP weapon take out the home city's electronics? Would that make the airships crash, or would they turn into gliders? (For practical purposes, the boats go dumb but many are able to be gotten to shore. The airships should crash.)
2) Should I just unleash an EMP event that has continental reach and accept the ramifications in terms of structural devastation to my city? If I do the latter, is there some way I can "safe" the walking cities against the EMP? They are essentially mechanical in nature, but their programming is electronic. However, they were also developed as a weapon of war, so I could have their programming be more like punch cards. The cities are powered with solar panelling so I don't think that's an issue. I may have some of the power for the airships and boats also be solar because then I can have spooky and mysterious LEDs flicker at the people who are studying a crash site.
3) Would whatever happens also take out any docked ships and grounded airships, or do I need a secondary problem to keep them from launching? (I could kill all the crews very easily, since the city that does this is going to be destroyed and abandoned.)
4) Would there be any lingering after-effects, two thousand years later, that a late-Middle-Ages civilisation would notice?
Please help me destroy my civilisation. They were jerks anyway.