I guess it depends on how you got caddy to begin with. If you used xcaddy, you have to update caddy the same way (recompile via xcaddy) otherwise you'll get the default binary which has no misc modules by default, which kinda sounds like what's happened but who knows for sure.
If you're feeling daring, you can try to compile caddy yourself with xcaddy, it's super easy.
Save your Caddyfile's (ultra important), and uninstall caddy. Install xcaddy (apt install xcaddy [or go install github.com/caddyserver/xcaddy/cmd/xcaddy@latest]). Then use xcaddy to compile caddy with the modules you need;
$ cd /tmp
$ xcaddy build --with github.com/caddy-dns/porkbun --with github.com/caddy-dns/cloudflare --with github.com/some-user/whatever-module
Caddy will build and be spit out in /tmp/caddy. Move it to /home/username/.local/bin or something, and make sure that directory is in your path. Don't forget to chmod +x caddy.
Run caddy like normal and see if this fixes your issue. If not, you'll likely have to try and older version of caddy (uninstall and specifically install the previous version or if you can't, use xcaddy with CADDY_VERSION to build a specific version with your modules), or wait until they push a fix for whatever they broke.