You can delete features by specifying feature IDs in the following way:

URL /index/:alias/:index/features/:ids
Method DELETE
URL parameters alias=[alphanumeric] specifies the name of the newly created DS. index=[alphanumeric] specifies the name of the newly created index. id=[alphanumeric] specifies IDs of features that are to be deleted. Separate multiple feature IDs with commas (,).
Success response Code: 200. Content: empty.
Error response Code: 400, which indicates that some required parameters are not specified. Content: empty.

Example: Delete the features whose IDs are 1 and 2 from the my_index index on my_ds.

 curl \
'localhost:8080/geoserver/geomesa/geojson/index/my_ds/my_index/features/1,2' -X DELETE