I don't think you are damaging the amp, as far as I know. With the pedal in the effects loop, you essentially process the signal AFTER the preamp stage, I believe, but before it goes to the poweramp, as opposed to in front of the amp, which controls how much signal actually gets "pre-amplified."
When you bring the pedal back, you are essentially sending less of the signal "X" to the speakers. Your preamp- and power amp-defined tonal characteristics won't change, since the gain stages have already affected the signal. This is also the way guitarist have done volume swells (Steve Morse for example) for a long time. This is the only way I know to do so with a pedal, in fact.
I think this is how it works, but anyone with different opinions/info, please chime in!