I spot-clay my vehicles all the time WITHOUT needing to reapply my protection. You DO, however, need to do it *GENTLY*. Some of my vehicles only get (multiple layers of) SG every 8-12 months, but I spot-clay them with almost every wash. I DO NOT have a problem with clay removing my protection. Even with (regular) waxes, if it's a good, fairly recent coat to begin with, the clay doesn't do much to it if you're careful.
You might want to put on another quick layer of S100, but your SG should be fine.
*If the roughness (that you're claying to remove) is UNDER your protection, then THAT'S a whole 'nother situation.*