AMP MUTE BUTTON QUESTION FOR THE ELECTRONIC GUYS AND GALS

i use a kill switch on my pedalboard as my first pedal. i switch basses a lot so i thought a kill switch would be better that using the mute on the amp.
when i use the mute on the amp and then unplug/plugin the bass i see the clipping light near the gain knob flashing. that harsh signal is still going through the amp but the speaker is just muted. is a signal just a signal and the amp just wants to amplify any signal going through it or are some signals worse than others? does the amp care?
is there any potential harm to the amp?

 

it is just a saturnworks pedal killswitch. first on my pedalboard. not sure how it is wired but i assume a standard killswitch.