There are two formats of an SSL certificate:

• PKCS12 - this is used by Xeams
• PEM - Used by Apache HTTPD and most likely by QNAP as well.

When a certificate file is created, files for both formats are saved on the disk. The PKCS12 format is saved in $INSTALL_DIR/config/letenc.pfx and the PEM is saved in $INSTAL_DIR/letsEncrypt/*.*

Assuming QNAP expects the PEM format, you will have to use that file and not *.pfx in QNAP. Moreover, everything is stored in a single file in case of PKCS12. However, PEM format uses multiple files to store private key and certs.