Agitation does not cause chlorine loss, in and of itself.
But, apropos of your situation, filters can accumulate massive bacterial growth. Judging from the odors I've encountered when opening filters in spring, I would guess that what's happening is anaerobic decomposition of oils and films on the sand - which is a good thing, I suppose.
However, the residual bacterial and decomp products could definitely create a chlorine demand.
-- This is a new idea for me. I've known about this, but never considered it. I have encountered 'greasy' sand on multiple occasions, and have considered that using the skimmers to add chlorine prevents this. But I'd never thought about 'cleaning' filters with bacterial digestion -- frankly, I'd never gotten past 'gagging' at the odor and black slime! --
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