It is possible that you will run into a rate limit for new-orders. I believe this does apply regardless of duplicate certificates. If that happens, please let us know and we can sort out the appropriate rate limit overrides. Unfortunately, most of the Let’s Encrypt staff is in North America and won’t be online for a few hours to fully resolve if that’s the issue.
You can create a maximum of 300 New Orders per account per 3 hours. A new order is created each time you request a certificate from the Boulder CA, meaning that one new order is produced in each certificate request. Exceeding the New Orders limit is reported with the error message
too many new orders recently.