Why is a long email not processed by Exim filters?
This is because Exim has a number of character length variable that will not process anything past that character length. This is to help remediate possible load or disk IO.
If you want to allow for longer emails to be processed the Exim message_body_visible setting would need to be increased. The Exim default is 500 but we increase it to 500 with our default installation. If you want to increase this you can in WHM using the Advanced Editor under Exim Configuration Manager. You can search for message_body_visible and change the value to 10000 for example. Then if an email is 10000 characters or less it will always be processed by the filter because it is seen text by Exim.