Step-by-step guide
You have to use the "by rank" syntax i.e. "#n#key". For example using the bufr_filter rules:
set #4#airTemperature = 3.14;
This sets the 4th instance of the key "airTemperature" to 3.14.
Note: Although you can use the "by condition" syntax for getting values of keys, this method cannot be used for setting such keys i.e. The following will not work:
# Does not work set /subsetNumber=4/airTemperature = 3.14; ## Error
Also see Setting keys by rank.