swapped out substrate, and am seeing ammonia now.

Some background:
29 gallon FOWLR, established 6 months. 2 clowns, 2 blue damsels SG 1.024 ph 8.1 I have been trying to drop our nitrates and get rid of the cyano growing everywhere. One the things mentioned that would help was switching our substrate to sand from crushed coral. So I bought 40 lbs of live sand and we proceeded to swap out the substrate.

I drained about 10 gallons of existing water in the tank into containers and put all the live rock in the buckets, we put the fish/invertabrates in a 5 gallon bucket with a single piece of live rock.

We drained the rest of the water, removed all substrate, replaces sand and refilled tank. We scrubbed some of the cyano off said live rock with a toothbrush.

This morning about 15 hours after the ammonia had spiked. It was 0 before and seems to be reading between 0 and 0.25 ppm. I am worried about the health of our clowns and damsels. What should I do ?

 

You removed part of your biological filter, it will should not take too much time for it to get up to speed again. Water changes, testing and products like Prime or even perhaps some Microbacter7 is about all you can do.

 

99% of the nitrifying bacteria live in biofilms on/in your LR, on tank walls, and on/in your substrate. You removed the substrate and took those bacteria out with it. Now there's a slight imbalance between Ammonia produced and the amount of bacteria present to process that.

Have no fear though. Their reproduction rate is tremendous and you'll be back down to zero very quickly.