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The following example removes all items with the “N/A” status:

Notice the .toList() in the loop, which avoids concurrency exceptions (deleting an item while lopping on it). An iterator can also be used.

import com.onresolve.scriptrunner.runner.customisers.WithPlugin;
import com.atlassian.jira.component.ComponentAccessor;
import com.atlassian.jira.issue.MutableIssue;
@WithPlugin("com.okapya.jira.checklist")
import com.okapya.jira.customfields.*;

// Retrieve the Custom Field Type for the Checklist Custom Field
def customFieldManager = ComponentAccessor.getCustomFieldManager();
def checklistCustomField = customFieldManager.getCustomFieldObject("customfield_10013");
def checklistCustomFieldType = (ChecklistCFType) checklistCustomField.getCustomFieldType();

// Remove N/A items from the Checklist
def issue = (MutableIssue) event.issue;
def ArrayList<ChecklistItem> existingChecklistValue = (ArrayList<ChecklistItem>) issue.getCustomFieldValue(checklistCustomField);
for (ChecklistItem item : existingChecklistValue.toList()) {
    // Remove all items with "Not Applicable" status 
    if (item.getStatusId() == "notApplicable") {
        existingChecklistValue.remove(item);
    }
}

// Update the issue with the checklist
checklistCustomFieldType.updateValue(checklistCustomField, issue, existingChecklistValue);
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