can I just leave it at that or do I need to do something else considering the lets encrypt auto-renew won't work because of the Cloudflare DNS ?
It won't work, so you will only need to remove the line from crontab ("sudo crontab -u bitnami -e"). In any case, even if it fails, the only thing happening is the command will throw an error but you won't see it, as it is executed by crontab.
I am worried the letsencrypt auto-renew might break something now that there are new Cloudflare)certificates in place.
You don't need to worry about that. The only case in which certificates are replaced is when you run generate-certificates.sh.
The script creates a symbolic link from certificates in /opt/bitnami/letsencrypt/certificates to /opt/bitnami/apache2/conf.
Therefore, as long as you don't place your certificates inside /opt/bitnami/letsencrypt/certificates you should be fine. Note you must NOT execute generate-certificates.sh anymore.
In any case if you're worried about this, just make a backup of the certificates and place them somewhere in your server.