I am breaking down some tanks as we are ,moving to a bigger location. 8 are already done and this is what i have done to minimize fish loss.
I removed all of the plants and put them in a plastic garbage bag.
then removed 50 % of the water and placed it in a larger buck, fishtank or whatever you have
Next I pushed all of the substrate up to one side making sure not to squish the shrimp that were in these tanks. Some of the 55 gal ones had over 300 shrimp. this makes a huge mess in your tank.
Here is the part that you actually need some equipment. I got a eheim canister filter and ran is 4 a few hours@ the end of the filter I put on a hydor sponge and placed that inside a container that was slightly to small for it to get a good seal. This basically cleared up the gunk pretty quick. I have a pic if you want to see it in action. I tried a diatom filter as well but it got clogged to quick.
After a few hours the tank cleared up pretty good. I then SLOWLY lowered the water in the tank to less than 1 inch, made a lind in the angled substrate so the shrimp had a barrier then started removing all of the substrate.
What you could do is @ that stage scoop up all of the shrimp and fish and put thiem with the regular water from your holding tank/spot.
Clean it up
Get all of the new substrate back in and aquascape.
Pour all of the holding tanks water and fish and shrimp back into the tank and over the neve few hours get it back up to full water. You can take longer if needed.