Solution:
1. cp /etc/cpanel_exim_system_filter /etc/cpanel_exim_system_filter_custom
2. edit /etc/cpanel_exim_system_filter_custom and remove the eml| from all the four noncommented lines that reference it.
3. log into WHM, click on Exim Configuration Editor, and change the system filter at the bottom from /etc/cpanel_exim_system_filter to /etc/cpanel_exim_system_filter_custom . Save the changes
Now Cpanel will use /etc/cpanel_exim_system_filter_custom, which if properly edited to remove the ‘eml|’ references in the particular lines will allow EML attachments to go through in the future.
Downside:
If Cpanel updates /etc/cpanel_exim_system_filter, you won’t benefit from the changes.