Lets encrypt problem with custom DocumentRoot template

[saxico]

Hi;

Since 1/2 weeks ago i'm having a problem when i try to enable LetsEncrypt cert with a custom template with diferent document root.

When i click to generate cert i get:
Error: Invalid response from http://XXX.com/.well-known/acme-challenge/XXX....

If i check the "public_html" folder i see that ".well-known" folder is created on public_html(default DocumentRoot) instead of my custom DocumentRoot. I supossed this is the problem.

The solution for me is disable my custom template, generate LetsEncrypt Cert, and then reenable my custom template, but i dont know if it will fail when the cert renew in next 3 months. Someone knows?

What i dont know is why is now failing, in the past i have activated so many LetsEncrypt certs with my custom template without problems. Can i solve this?

Thanks

Edit: I'm using Ubuntu 16 (apache+nginx) mainly, but i have the same problem with other server with Debian 8(only apache).

[grayfolk]

If i check the "public_html" folder i see that ".well-known" folder is created on public_html(default DocumentRoot) instead of my custom DocumentRoot. I supossed this is the problem.

Just create symlink from /public_html/.well-known to /your_docroot/.well-known