Electrical engineer here. There is nothing odd about putting a PCB in an oven. Any surface mount PCB is assembled using a reflow oven which heats all the components, as well as the PCB itself, several degrees for quite some time up to the 'soak' temperature, which is 150 °C.
After that, the PCB (and components, still not soldered but held down with solder paste) are heated up to the reflow temperature, which for lead-free processes (i.e., all of them) is 245 °C. After this point, they are held at that temperature for 60-90 seconds to allow the solder to completely reflow. Note, this is not time spent with the oven temperature that hot - this is time the entire PCB, which edge to edge has reached 245 °C, spends at that temperature.
There is absolutely nothing wrong with, nor anything odd about putting a PCB in an oven or otherwise getting it hotter than it's glass transition temperature. Doing so is a key part of their commercial assembly into electronics and has already been done to every PCB you own.
Please ignore the 'accepted' answer - it's incorrect.
PCBs are usually made out of glass epoxy composite (FR4) with a glass transition temperature of 140°C. There are high heat varieties with a glass transition temperature of 170°C. I do not know which variety the Prusa MK2/MK2S uses specifically, but FR4 doesn't have a 'sharp' glass transition anyway, so you want to err on the side of hot regardless of the specific type. Get it nice and cozy at at 190-200 °C, and increase the temperature until it unwarps. The solder's liquidus is about 220°C, so you should try to keep 20 °C shy of this just because kitchen oven thermostats are not to be trusted.
I own a MK2S, and have personally heated my heat bed up to above the glass transition temperature of PEI (don't ask) which is 217°C, and this was not a problem (well, except for the PEI but again, don't ask). It didn't suffer any ill effects, nor did I expect it too. I'm printing on it right now, as I type this. It's perfectly fine to heat it up that hot. That was the entire reason FR laminate was even made - to be rigid and to tolerate being hot. Solder ain't gonna melt itself.
Note, however, you will need to remove the PEI/Ultem sheet as well as the adhesive before you do this. Prusa has instructions on how, look under replacing the PEI print surface.
Now, as for the actual procedure, the pcb isn't going to magically just become flat. You have to force it to flatness. Flatten it into submission. It will only be as flat as the hopefully flat surface it is resting on. And, given the gradual transition of the material, it isn't going to exactly become super pliable even when a good deal past its glass transition temperature.
What you ideally want is two plates of aluminum large enough to sandwich it between. Or steel, or any metal. They need to be thick enough to not flex so they are very flat. A pizza stone, if you can find one that is flat, or a slab of granite also works. I know none of these are exactly 'just laying around the house' type objects, but really any flat surface that will tolerate the heat that you can rest the pcb on is acceptable. (Kids - ask your parents first)
The only problem is it will likely not unwarp itself under its own weight. You'll need to put a large flat thing on top of it too, and either have it be heavy, or add heavy things on top of your large flat thing. You want to make a heat bed sandwich. Also, it needs to be shielded from the oven heating elements (be they electric or gas), as these will radiate heat a lot hotter than the oven temperature when they turn on. Don't worry - aluminum foil is enough to shield anything from the heat, but again, you should have something very flat and substantial on top.
Oh, and remove the screw hole sockets from the PCB. They just need a hex key and some pliers to unscrew. Don't lose the lock washers.
Anyway, the above procedure, while definitely a pain, will restore (or if it was always warped, imbue for the first time) flatness as good as the flat things it is sandwiched between.
The flatness of kings.
This isn't exactly unknown either. People do it. It works.