There's no way to avoid stressing your shrimp one way or another. How about a partial change, replacing quadrants or 1/8ths at a time?
I think Lauralee spoke of a technique where she pours new substrate down a vacuum tube into the places she wants it to fall.
Maybe that could work and reduce the need to re-acclimate livestock.
I've only rebuilt once. Filled a few 5G buckets with water ($3 each at Lowes), put plants in one, fish in the others and did the rebuild. Poured old water in,backfilled with new and everybody was fine. Took about 4 hours. No invertebrates though. And no significant change in water chemistry due to the substrate, so you would still have to deal with a slower acclimation than I did. Maybe one way to accomplish that is to put some substrate into a container or two prior, with something for circulation, to create your "new water", then use that water for acclimation in parallel with you're rebuild.
Rebuild isn't such a big deal when you have a filter that is still mature (don't decide to clean it the same day btw), but a significant water chemistry change and inverts makes it more challenging.
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