It could be a problem with your rewrite rule. You need to maintain the configuration so that when you put a file in /.well-known/acme-challenge under your document root directory (as previously specified to the Let’s Encrypt client), that same file’s contents will get served on your web site at that location.
I am not particularly familiar with mod_rewrite so I don’t know how to suggest fixing this if this is indeed the problem. My first suggestion would be "learn mod_rewrite". (or, start a new topic here about how to make Apache RewriteRule exceptions?)