Okay, I must have expressed myself badly. I don't have/use a sponge filter, I am using a canister filter. I do have a skimmer and 2 pwoer heads also.

Yes, I do plan on replacing all the crushed coral.
No, I do not plan on mixing the two substrates( other than maybe some small stray pieces. Like I said in the original post, I have already the substrate in half the tank. I scooped out what I could, then used a hose the syphon to clean out that half.
Yes, there was quite a cloud. Quite clear today. I took a baster and used it to blow the live rock and soft corals clean.

When I cleaned the used coral that I removed, so that it would not stink up the place. I had the coral in a 5 gallon pail in the laundry tub and ran water through while mixing the my hands. That produced green frouth and the same type oder that I was smelling from the tank.

Another concern of mine. This is a 55 gallon tank on the upper shelf of an iron stand. Below is a 40 gallon FW tank lit by 130 watt compact light strip. While I would not say that the light gives off a lot of heat, it does get warm. Do you think that this heat will couse a problem with the substrate. I thought of something last night but forgot to test it this morning. I will stick my digital thermonitor probe down into the bottom of the subatrate to measure the temp. I get back to you on the morning temp( when the lite below has been off for 8 or so hours) and in the evening when that lite has been on 12 hours.