Does it make sense to place a looping pedal at the end of my effects loop?

Will this alter the sound being stored by the looping pedal when I adjust the amp settings via the amplifier's footswitch (i.e. I switch from rhythm channel to Lead channel)?

I am using a Digitech JamMan and a MesaBoogie DC-10, if that matters. I am new to both Looping pedals AND Effects Loops. I am willing to experiment but i certainly don't want to damage my equipment.