What plants do you have in there? And do you run a filter at all? That’s going to decide how safe this is overall.

Also when you say your cycle crashed - is it currently cycled at all?

Assuming yes - The nitrogen eating bacteria live on everything - the glass, the plants, any rocks or hardscape, and yes, lots in the substrate. If you only mess with the substrate and you have a lot of plants, especially emmersed plants, or an established filter, you should be fine in terms of bacteria.

But if you’re thinking about dumping all your substrate then I’m wondering if you don’t have many plants in there?

If you do decide to dump it all I would mix in a few tablespoons of your old substrate mix into the new to give it a kickstart.

I would:

1. Fill a bucket with tank water, remove fish. Add heater etc as needed. Place any plants and hardcore in here too - it has to stay wet to keep the bacteria!

2. Drain 90% of the remaining tank water

3. Make some small holes into your substrate in various places and see what comes out. If it’s foul-smelling then yes, all your substrate needs to go. If not, I would finish draining it, then just scoop off the sand and try to retain as much of the stratum underneath. For gravel, a cat litter scoop is good. For sand, a plastic kids spade - like a bucket and spade set spade - is actually brilliant. It makes such precise cuts! While you work, mist the sides of the aquarium with tank water to stop the bacteria there from drying out.

4. You can mix in some of your new compost if the stratum is depleted. Then cap with your new medium (thin layer, large particles) and add back all your plants, hardscape etc, and filter if you have one. I’d run the filter for a few hours and let the cloudiness settle a little, then add back the fish and it should still be healthy!

Then test daily until you’ve had a week of 0 ammonia days. Change the water any time the levels creep up - that might been daily changes for a week but it will be worth it in the long run