It's a different rate limit - 5 per week for an exact duplicate set of domains:
Renewals are treated specially: they don’t count against your Certificates per Registered Domain limit, but they are subject to a Duplicate Certificate limit of 5 per week. Note: renewals used to count against your Certificate per Registered Domain limit until March 2019, but they don’t anymore.
A certificate is considered a renewal (or a duplicate) of an earlier certificate if it contains the exact same set of hostnames, ignoring capitalization and ordering of hostnames. For instance, if you requested a certificate for the names [
www.example.com,example.com], you could request four more certificates for [www.example.com,example.com] during the week. If you changed the set of hostnames by adding [blog.example.com], you would be able to request additional certificates.
Since the private keys for your duplicate certificates are destroyed, your choices are either to wait ~32 hours or issue a certificate with a different set of domains.
Edit: you can more clearly see the duplicate certificate rate limit in effect here: Let's Debug Toolkit