In the future, please read the complete error message, including any links in it. The rate limit documentation page clearly states that what you were asking initially, isn't possible.
Also, in the future, please be more careful with the precious resources of Let's Encrypt. While the certificates might be free for you, it costs Let's Encrypt a considerable amount of money to make this happen! And more certificates being issued, means more costs for all the infrastructure. By carelessly deleting your VM without backing up the certificates, you're wasting Let's Encrypt resources. Hence the rate limits and hence no possibility to reset them.