The magnets are on the rotor (where the spokes are), not the stator.
However, the stator teeth (the thin metal layers between the windings) are usually the same width as the magnets, so I'm guessing that's what you mean, and why you need to widen the existing rotor to match?
If so, that's ok...but silicone is not sufficient to "fill the gap" by itself, as it wont' transmit stresses from rotor to axle the way the covers are designed to.
what it means is that the bolts securing the cover will do all of that load transfer, and they'll break (or unscrew and fall out, or both) from the repeated rotary bending actions, disconnecting the covers from the rotor, makign the rotor magnets roll on the actual stator laminations.
you'll need to make a solid, hard ring to fill that gap. lexan or plexiglass or a number of other things can be used, if you can't get metal rings made. the rings will need to have a recess for the lip of the covers to go into, and a lip of their own just like it to go into the rotor, to help transfer the loads into teh covers so they can transfer to the axle.
you also need rings on the axle between the cover bearings and the axle shoulder of the stator, if there is any gap there, or else the wheel can move side to side on the axle while riding, and allow the windings to strike the covers, and destroy the new stator.