You won't lose any data when you run this command but make a back up before!

hmm, we upgraded our qa environment, and we only have a single identity in our DB now. Unfortunately we didn't back anything up as it was QA (doh!).

You're probably the same person but posting it here: https://github.com/ory/kratos/discussions/2104#discussioncomment-1907483

thanks for posting that. I've verified all the identities are in the DB, and for some reason the kratos api just wasn't returning them, however it is now. Thank you for following up!