So it will actually be the id_rsa file within that .ssh folder that you have been deleting. DevKinsta basically creates a shortcut to that folder/file.
I asked if you were using Hyper-V because that’s the only other time I’ve seen Windows mess up the permissions of this file: DK0029 Error - Unprotected private key file
I was also wondering if how you installed DevKinsta (for just the root user or all users) was affecting this.