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If you importing a checklist into issues that may already contain checklists- you need to additionally sync the "Checklists" field with com.railsware.SmartChecklist.checklist issue property, which now is the main data source.

You can utilize any available tools for that.

E.g. Automation for Jira for Server

The approach is the following 

1. Setup the "Scheduled" event rule
   

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2. Set the execution time 

3. Set proper JQL function to update only the needed issues 

4. "Set entity property" Action to update "com.railsware.SmartChecklist.checklist" from "Checklists" custom field

5. Save the Function and make sure it is enabled for a short time that you need to actually sync the values

6. Once you proceed with Bulk import - "Run Rule" manually 

7. That way your current checklist will get data from imported CSV based on the "Checklists" custom field

We are working on implementing the easiest way to synchronize checklist storages. So update of the "Checklists" custom field will automatically trigger checklist update even if there already were some values present.