As far as I understand, provided you do not issue any wipe command, you can safely overwrite a kernel. I routinely.use Mobile Odin Pro for that.
On my device, I installed 4.0.4 stock German LRG upon 4.0.3 with SpeedMod, after wiping cache and Dalvik cache while still in SpeedMod kernel, which is safe.
Then CfRoot kernel over 4.0.4 stock kernel (which is unsafe, but since I didn't wipe there was no risk).
Then, lastly, SpeedMod k3-9 over CfRoot.

SpeedMod seems notably quicker than CfRoot out stock... When I have my inlaw Note available, which is 4.0.4 with CfRoot, I'll try a head-to-had comparison.