Let's Encrypt doesn't issue encrypted certificates. I think your question might be better suited on a support forum specifically for Windows based webservers.
Also, Windows 2008 R2 is an Operating System (OS), not the name of any webserver software specifically.
From a Let's Encrypt perspective, the certificates are send "plain text" (over a secure TLS connection that is) using the ACME protocol.
It might be that your ACME client supports bundling the private key, certificate and perhaps chain into a single, password encrypted file. But that's something the ACME client would do, not the ACME server (i.e.: Let's Encrypt).
So based on the very limited information you have provided I believe this is not the right Community for your question.
Maybe there are some volunteers on this Community who could help you with your issue, but as crystal balls don't exist, you would need to provide a lot more information than the current info. E.g., you've deleted almost every question of the questionnaire and frankly I'm very puzzled why you did so. It only makes helping you, if we even can, harder. Personally I don't have any experience with Windows Server (luckily), so I couldn't help you even if I wanted to, but with so little information to work with, well, to be honest, it might make fellow volunteers decide not even to put in the effort.