Could you be clearer about what you mean by "domain pointers"? Are these DNS CNAME records? Are they all under the same domain?
What you experienced is probably a misconfiguration problem rather than anything to do with the Let's Encrypt rate limits. In particular, when a rate limit is hit, you get an error when trying to get subsequent certificates. Nothing is done to remove or invalidate any existing certificates.
If you're willing to list these names in larger certificates, you can list up to 100 names in a single certificate, so you could cover 120 names with just two certificates, rather than 12. There are no limits that would require only listing 10 names per certificate.
Maybe you could tell us more about your software and hosting environment and what means you used to obtain and install these certificates?