I would expect the warranty to be more or less unaffected, outside of the emitter mod itself. The emitter is probably the least prone to failure point on the whole unit. You only need to remove the reflector, too, which is clearly acceptable for a user to do, based on HDS' history of offering different reflectors as accessories, which are still compatible with the current lights. The whole epoxied electronics and heatsinking assembly is untouched.
IANAL, but I'm pretty sure that's even legally the case, in the US (FI, if your switch contacts start messing up, you can't be denied a warranty claim due the LED swap, since it isn't related to the defect), not that I would expect much of a hassle.
You can even send it in for recalibration, after an utter swap, unless things have changed recently.
