Issue
Filtering the Delete Multiple Items action on a Yes/No SharePoint column doesn't delete the correct items.
Resolution
Replace the Delete Multiple Items action with a Query List action that filters on the Yes/No column value. Then, loop through the query results and use the Delete Item action to delete one item at a time. A workflow export is attached as an example.
Additional Information
This issue is pending a fix in a later release.
Related Links
Query List
https://help.nintex.com/en-US/nintex2016/current/#sp2016/Workflow/ActionsCore/QueryList.htm
For Each Loop
https://help.nintex.com/en-US/nintex2016/current/#sp2016/Workflow/ActionsCore/ForEach.htm
Delete Item
https://help.nintex.com/en-US/nintex2016/current/#sp2016/Workflow/ActionsCore/DeleteItem.htm