That one has an easy fix: store secrets in a separate repo that you never roll back. That's not the reason to avoid storing secrets in git. You might be giving some junior dev here the idea that if they can solve this issue, then storing secrets in git will be ok. Obviously it's not; it's still a bad idea after you've solved this minor annoyance and, indeed, this annoyance had nothing to do with the security reason why you don't store secrets in git.