The root certificate is located at /data/caddy/pki/authorities/local/, so it should be persistent.
Edit: I noticed the certificate’s last modified date is from March 22nd, so it’s definitely the same one as before. Not sure why it had issues trusting it.
That was for Caddy #2, but Caddy #1 shares the same bind mounts.
Regardless, your last question made me realize my mistake. I was accidentally copying over the leaf certificate instead of the root certificate to Caddy #1. This is why it lost trust after 12 hours! I was clearly not paying attention haha. Thank you again.