Letsencrypt on OS 6.7

I've installed certificates via Letsencrypt for my domain.

I followed the procedure described in another discussion you can find under Using Your Readynas.

All seems to work fine, but when I access the admin console via the local IP adress, the certificates do not match.

Probably because the self-singed certificates were replaced by ones that do not match with the local IP  adress.

Everything else seems to work fine except for Shellinabox and Sickbeard.

I decided to uninstall both and than to reinstall them.

Sickbeard I was able to uninstall, but the uninstall of Shellinabox failed.

Using Putty I noticeed that the shellinabox folder under apps still exists and has a certificate.pem file in it.

Should I delete the file?

Should I try to add the avaiable self signed certificates to apache2.pem and will this solve this issue and also the issue with access via my local IP address?

But will my domain than also stil work properly?