However, for some reasons, I had to set up again and again. In my last installation, I started to receive a warning "This site is not safe". When I use a different SSL instead of Let's Encrypt, this problem disappeared.
Ah. What purpose people think obfuscating their domain name serves is a mystery to me. But according to crt.sh, the last cert issued for that domain was on 30 Sep, and the last before that on the 29th--so the duplicate cert limit shouldn't apply. Though crt.sh could be behind again.