The ammonia may be from disrupting the sand bed, but it's not directly from the cyano
, or removing it. How much sand do you have left?
If you are planning to add more I would do it in small amounts over a period of time, so not to suffocate whatever is living in the higher oxygen areas of the sand bed. Covering the entire bed with an inch of sand would surely kill off some, if not all, of whatever you have living in it.