did you all quantify any of the findings - undisclosed discrepancies with the preregistration, etc.? working with a journal to investigate this issue and try to address it; any data or guidance would be helpful (or workflow steps you used or recommend)

It’s a commentary not an empirical paper, so no, but we include guidance and a checklist for authors. In most cases the Open Science Advisor works 1-on-1 with the author to resolve discrepancies before awarding a badge.