When you execute stop_etl.nsh following is the sequence of events that occur-
1) Removal of running ETL sessions in Unix/Windows
2) Removing exstat files for given site id
3) Removal of .LCK file from bin folder for that site
4) Removing child processes spawned by the run_etl for given site
5) Resetting ETL [ETL_LAST_RUN] table to ForceError
Hope this answers your query.