You could probably improve your copying script to recursively go through all directories under a base directory and search for ‘.crt’ files.
Additionally, you could combine it with some openssl syntax to only copy certificates that have their issue date most recently to the current date, preventing expired or old certificates to be copied when both zerossl and letsencrypt locations have certificates for the same domain name.
I have recently wrote a script that returns certificates and their end dates because I consume that in monitoring, maybe you can adjust that to copy certificates instead?