Another option is to use the DNS Challenge. This can work well in this situation if you have API control of the DNS. If this is an option note the acme.sh ACME client supports many more DNS API's than certbot. If you'd provided details on your config we could give more specific advice.
Below is a thread which discussed various methods for dealing with multiple servers operating behind a load balancer. It is not exactly your case but perhaps helpful anyway
It's also important to realize that the Let's Encrypt servers are the ones making the challenge requests. There will be (currently) four requests from different locations around the globe. The ACME client is just making a request for a cert from the LE Server. The client has no control over that challenge process. This doc page explains this in more detail