Please review the rate limit documentation. There are a few you could run into while doing this, depending on your implementation.
You will probably want to clear each authorization before moving to the next, or at least clear a handful at a time. If these are all subdomains of a single public suffix, you may need to add several of these (~40) to each certificate as subject alternate names, as you can only issue 20 certificates for any given domain per week, but each can have up to 100 subject alternate names for 2000 subdomains per week.
The integration guide may also prove helpful for you: