If a particular item is no longer available in the catalog, then you need to call the Delete API to get it removed from the index. 

Request URL: https://indexing-api.ksearchnet.com/v2/batch/delete
Request Method: PUT
Request Headers:
X-KLEVU-TIMESTAMP=2023-06-19T00:00:00.000Z
X-KLEVU-APIKEY=klevu-1234567890
X-KLEVU-AUTH-ALGO=HmacSHA384
Content-Type=application/json
Request body:
{
  "ids": [
    "3", "2", "men-shirts"

If deleting a variant from a complex product causes any of the fields to change for other variants, e.g. startPrice and toPrice, then you need to index the other variants again.

Deletes

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