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At risk of stating the obvious (and assuming we are talking about wells in unconsolidated sediments), prior to undertaking shock dosing of wells, it is important to be sure that there is no further risk of well contamination (e.g. no flooded latrine pits in the vicinity and low risk of contaminants remaining resident in the sediments surrounding the wells), otherwise the shock dosing will be a waste of time and money in addition to providing the dangerous illusion that the wells have been cleaned up post dosing.
In terms of shock treatment of wells there is this https://www.who.int/water_sanitation_health/hygiene/envsan/tn01/en/index.html
Also included are some draft docs from the cluster in water supply and sanitation in floods